I don't think that theory stands. Here are the two -T reports of the same files I used earlier. It looks to me as though the main data block is at the end in both cases. Interesting to note that MP3TAG seems to add an extra empty atom (4096 bytes) just before the main data block.

______________________________________________________________________
```
C:\>atomicparsley "_Made by Winamp.m4a" -T
Atom ftyp @ 0 of size: 24, ends @ 24
Atom moov @ 24 of size: 25135, ends @ 25159
Atom mvhd @ 32 of size: 108, ends @ 140
Atom iods @ 140 of size: 42, ends @ 182
Atom trak @ 182 of size: 22635, ends @ 22817
Atom tkhd @ 190 of size: 92, ends @ 282
Atom mdia @ 282 of size: 22535, ends @ 22817
Atom mdhd @ 290 of size: 32, ends @ 322
Atom hdlr @ 322 of size: 33, ends @ 355
Atom minf @ 355 of size: 22462, ends @ 22817
Atom smhd @ 363 of size: 16, ends @ 379
Atom dinf @ 379 of size: 36, ends @ 415
Atom dref @ 387 of size: 28, ends @ 415
Atom stbl @ 415 of size: 22402, ends @ 22817
Atom stsd @ 423 of size: 106, ends @ 529
Atom mp4a @ 439 of size: 90, ends @ 529
Atom esds @ 475 of size: 54, ends @ 529
Atom stts @ 529 of size: 24, ends @ 553
Atom stsz @ 553 of size: 21712, ends @ 22265
Atom stsc @ 22265 of size: 40, ends @ 22305
Atom stco @ 22305 of size: 512, ends @ 22817
Atom udta @ 22817 of size: 1500, ends @ 24317
Atom meta @ 22825 of size: 1018, ends @ 23843
Atom hdlr @ 22837 of size: 33, ends @ 22870
Atom ilst @ 22870 of size: 973, ends @ 23843
Atom ---- @ 22878 of size: 187, ends @ 23065
Atom mean @ 22886 of size: 28, ends @ 22914
Atom name @ 22914 of size: 20, ends @ 22934
Atom data @ 22934 of size: 131, ends @ 23065
Atom ©nam @ 23065 of size: 39, ends @ 23104
Atom data @ 23073 of size: 31, ends @ 23104
Atom ©wrt @ 23104 of size: 38, ends @ 23142
Atom data @ 23112 of size: 30, ends @ 23142
Atom ---- @ 23142 of size: 124, ends @ 23266
Atom mean @ 23150 of size: 30, ends @ 23180
Atom name @ 23180 of size: 16, ends @ 23196
Atom data @ 23196 of size: 70, ends @ 23266
Atom ---- @ 23266 of size: 210, ends @ 23476
Atom mean @ 23274 of size: 30, ends @ 23304
Atom name @ 23304 of size: 16, ends @ 23320
Atom data @ 23320 of size: 156, ends @ 23476
Atom ©ART @ 23476 of size: 31, ends @ 23507
Atom data @ 23484 of size: 23, ends @ 23507
Atom aART @ 23507 of size: 31, ends @ 23538
Atom data @ 23515 of size: 23, ends @ 23538
Atom ©alb @ 23538 of size: 55, ends @ 23593
Atom data @ 23546 of size: 47, ends @ 23593
Atom ©gen @ 23593 of size: 41, ends @ 23634
Atom data @ 23601 of size: 33, ends @ 23634
Atom ©day @ 23634 of size: 28, ends @ 23662
Atom data @ 23642 of size: 20, ends @ 23662
Atom disk @ 23662 of size: 30, ends @ 23692
Atom data @ 23670 of size: 22, ends @ 23692
Atom ---- @ 23692 of size: 83, ends @ 23775
Atom mean @ 23700 of size: 31, ends @ 23731
Atom name @ 23731 of size: 21, ends @ 23752
Atom data @ 23752 of size: 23, ends @ 23775
Atom trkn @ 23775 of size: 32, ends @ 23807
Atom data @ 23783 of size: 24, ends @ 23807
Atom ©too @ 23807 of size: 36, ends @ 23843
Atom data @ 23815 of size: 28, ends @ 23843
Atom hnti @ 23843 of size: 474, ends @ 24317
Atom rtp @ 23851 of size: 466, ends @ 24317
Atom trak @ 24317 of size: 429, ends @ 24746
Atom tkhd @ 24325 of size: 92, ends @ 24417
Atom mdia @ 24417 of size: 305, ends @ 24722
Atom mdhd @ 24425 of size: 32, ends @ 24457
Atom hdlr @ 24457 of size: 33, ends @ 24490
Atom minf @ 24490 of size: 232, ends @ 24722
Atom nmhd @ 24498 of size: 12, ends @ 24510
Atom dinf @ 24510 of size: 36, ends @ 24546
Atom dref @ 24518 of size: 28, ends @ 24546
Atom stbl @ 24546 of size: 176, ends @ 24722
Atom stsd @ 24554 of size: 76, ends @ 24630
Atom mp4s @ 24570 of size: 60, ends @ 24630
Atom esds @ 24586 of size: 44, ends @ 24630
Atom stts @ 24630 of size: 24, ends @ 24654
Atom stsz @ 24654 of size: 20, ends @ 24674
Atom stsc @ 24674 of size: 28, ends @ 24702
Atom stco @ 24702 of size: 20, ends @ 24722
Atom tref @ 24722 of size: 24, ends @ 24746
Atom mpod @ 24730 of size: 16, ends @ 24746
Atom trak @ 24746 of size: 413, ends @ 25159
Atom tkhd @ 24754 of size: 92, ends @ 24846
Atom mdia @ 24846 of size: 313, ends @ 25159
Atom mdhd @ 24854 of size: 32, ends @ 24886
Atom hdlr @ 24886 of size: 33, ends @ 24919
Atom minf @ 24919 of size: 240, ends @ 25159
Atom nmhd @ 24927 of size: 12, ends @ 24939
Atom dinf @ 24939 of size: 36, ends @ 24975
Atom dref @ 24947 of size: 28, ends @ 24975
Atom stbl @ 24975 of size: 184, ends @ 25159
Atom stsd @ 24983 of size: 84, ends @ 25067
Atom mp4s @ 24999 of size: 68, ends @ 25067
Atom esds @ 25015 of size: 52, ends @ 25067
Atom stts @ 25067 of size: 24, ends @ 25091
Atom stsz @ 25091 of size: 20, ends @ 25111
Atom stsc @ 25111 of size: 28, ends @ 25139
Atom stco @ 25139 of size: 20, ends @ 25159
Atom mdat @ 25159 of size: 1007411, ends @ 1032570
------------------------------------------------------
Total size: 1032570 bytes; 99 atoms total. AtomicParsley version: 0.9.0 (utf16)
Media data: 1007411 bytes; 25159 bytes all other atoms (2.437% atom overhead).
Total free atom space: 0 bytes; 0.000% waste.
```

______________________________________________________________________
```
C:\>atomicparsley "_No visible tags on Pioneer.m4a" -T
Atom ftyp @ 0 of size: 24, ends @ 24
Atom moov @ 24 of size: 25131, ends @ 25155
Atom mvhd @ 32 of size: 108, ends @ 140
Atom iods @ 140 of size: 42, ends @ 182
Atom trak @ 182 of size: 22635, ends @ 22817
Atom tkhd @ 190 of size: 92, ends @ 282
Atom mdia @ 282 of size: 22535, ends @ 22817
Atom mdhd @ 290 of size: 32, ends @ 322
Atom hdlr @ 322 of size: 33, ends @ 355
Atom minf @ 355 of size: 22462, ends @ 22817
Atom smhd @ 363 of size: 16, ends @ 379
Atom dinf @ 379 of size: 36, ends @ 415
Atom dref @ 387 of size: 28, ends @ 415
Atom stbl @ 415 of size: 22402, ends @ 22817
Atom stsd @ 423 of size: 106, ends @ 529
Atom mp4a @ 439 of size: 90, ends @ 529
Atom esds @ 475 of size: 54, ends @ 529
Atom stts @ 529 of size: 24, ends @ 553
Atom stsz @ 553 of size: 21712, ends @ 22265
Atom stsc @ 22265 of size: 40, ends @ 22305
Atom stco @ 22305 of size: 512, ends @ 22817
Atom trak @ 22817 of size: 429, ends @ 23246
Atom tkhd @ 22825 of size: 92, ends @ 22917
Atom mdia @ 22917 of size: 305, ends @ 23222
Atom mdhd @ 22925 of size: 32, ends @ 22957
Atom hdlr @ 22957 of size: 33, ends @ 22990
Atom minf @ 22990 of size: 232, ends @ 23222
Atom nmhd @ 22998 of size: 12, ends @ 23010
Atom dinf @ 23010 of size: 36, ends @ 23046
Atom dref @ 23018 of size: 28, ends @ 23046
Atom stbl @ 23046 of size: 176, ends @ 23222
Atom stsd @ 23054 of size: 76, ends @ 23130
Atom mp4s @ 23070 of size: 60, ends @ 23130
Atom esds @ 23086 of size: 44, ends @ 23130
Atom stts @ 23130 of size: 24, ends @ 23154
Atom stsz @ 23154 of size: 20, ends @ 23174
Atom stsc @ 23174 of size: 28, ends @ 23202
Atom stco @ 23202 of size: 20, ends @ 23222
Atom tref @ 23222 of size: 24, ends @ 23246
Atom mpod @ 23230 of size: 16, ends @ 23246
Atom trak @ 23246 of size: 413, ends @ 23659
Atom tkhd @ 23254 of size: 92, ends @ 23346
Atom mdia @ 23346 of size: 313, ends @ 23659
Atom mdhd @ 23354 of size: 32, ends @ 23386
Atom hdlr @ 23386 of size: 33, ends @ 23419
Atom minf @ 23419 of size: 240, ends @ 23659
Atom nmhd @ 23427 of size: 12, ends @ 23439
Atom dinf @ 23439 of size: 36, ends @ 23475
Atom dref @ 23447 of size: 28, ends @ 23475
Atom stbl @ 23475 of size: 184, ends @ 23659
Atom stsd @ 23483 of size: 84, ends @ 23567
Atom mp4s @ 23499 of size: 68, ends @ 23567
Atom esds @ 23515 of size: 52, ends @ 23567
Atom stts @ 23567 of size: 24, ends @ 23591
Atom stsz @ 23591 of size: 20, ends @ 23611
Atom stsc @ 23611 of size: 28, ends @ 23639
Atom stco @ 23639 of size: 20, ends @ 23659
Atom udta @ 23659 of size: 1496, ends @ 25155
Atom hnti @ 23667 of size: 474, ends @ 24141
Atom rtp @ 23675 of size: 466, ends @ 24141
Atom meta @ 24141 of size: 1014, ends @ 25155
Atom hdlr @ 24153 of size: 34, ends @ 24187
Atom ilst @ 24187 of size: 968, ends @ 25155
Atom trkn @ 24195 of size: 32, ends @ 24227
Atom data @ 24203 of size: 24, ends @ 24227
Atom disk @ 24227 of size: 32, ends @ 24259
Atom data @ 24235 of size: 24, ends @ 24259
Atom ©gen @ 24259 of size: 41, ends @ 24300
Atom data @ 24267 of size: 33, ends @ 24300
Atom ©alb @ 24300 of size: 55, ends @ 24355
Atom data @ 24308 of size: 47, ends @ 24355
Atom ©ART @ 24355 of size: 31, ends @ 24386
Atom data @ 24363 of size: 23, ends @ 24386
Atom aART @ 24386 of size: 31, ends @ 24417
Atom data @ 24394 of size: 23, ends @ 24417
Atom ---- @ 24417 of size: 122, ends @ 24539
Atom mean @ 24425 of size: 28, ends @ 24453
Atom name @ 24453 of size: 16, ends @ 24469
Atom data @ 24469 of size: 70, ends @ 24539
Atom ---- @ 24539 of size: 208, ends @ 24747
Atom mean @ 24547 of size: 28, ends @ 24575
Atom name @ 24575 of size: 16, ends @ 24591
Atom data @ 24591 of size: 156, ends @ 24747
Atom ---- @ 24747 of size: 187, ends @ 24934
Atom mean @ 24755 of size: 28, ends @ 24783
Atom name @ 24783 of size: 20, ends @ 24803
Atom data @ 24803 of size: 131, ends @ 24934
Atom ---- @ 24934 of size: 80, ends @ 25014
Atom mean @ 24942 of size: 28, ends @ 24970
Atom name @ 24970 of size: 21, ends @ 24991
Atom data @ 24991 of size: 23, ends @ 25014
Atom ©nam @ 25014 of size: 39, ends @ 25053
Atom data @ 25022 of size: 31, ends @ 25053
Atom ©too @ 25053 of size: 36, ends @ 25089
Atom data @ 25061 of size: 28, ends @ 25089
Atom ©wrt @ 25089 of size: 38, ends @ 25127
Atom data @ 25097 of size: 30, ends @ 25127
Atom ©day @ 25127 of size: 28, ends @ 25155
Atom data @ 25135 of size: 20, ends @ 25155
Atom free @ 25155 of size: 4096, ends @ 29251
Atom mdat @ 29251 of size: 1007411, ends @ 1036662
------------------------------------------------------
Total size: 1036662 bytes; 100 atoms total. AtomicParsley version: 0.9.0 (utf16)
Media data: 1007411 bytes; 29251 bytes all other atoms (2.822% atom overhead).
Total free atom space: 4096 bytes; 0.395% waste. Padding available: 4096 bytes.
------------------------------------------------------
```

______________________________________________________________________
There appear to be far larger structural changes than I would have expected for a mere 'do nothing' save. It's all fairly consistent until we get to approx 22817 into the file; then it all gets a bit wild.

Moderation: Added codeboxes to reduce size.