Not possible to save track numbers with leading zero in m4a

Not really.
The mp4 tags do not allow leading zeros as the track number is really a number and not a "numeric string" as for mp3 files.

If you want to adapt the display in MP3tag, you could try
$num(%track%,2)for the setting in "Value" for the column definition.
(This will not show the number total tracks, though).

See also here: