Why MP4 Tag vs ID3?

So, the MP3Tag app now reveals my (mostly iTune purchased) files as MP4 with no cover art or song information? Using a different product (TagScanner) I'm able to retrieve this data and imbed it into the individual files and they then appear as ID3 in MP3Tag and normally in Windows iTunes. Within iTunes (Windows) the art and track info appears "normally" in either the MP4 or ID3b2.3 file version. I've had problems getting cover art onto my iOS devices from the PC so I am converting all MP4 files to ID3. I hope I'm not hosing things for when I sync them over to iPAD. What made the previously fine ID3 tags change to MP4? Will iOS stomp over the tag amendments I've made? Thx for advice.

The ID3 tags are for MP3 files.
MP4 files have "atoms", I think.
So, I am not sure what you do.
Do you convert the MP4 files to MP3?

Previously, I was able to use mp3tag to clean up iTunes files that had lost their cover art, or to clean MP3 files ripped from CD and imported to iTunes. One day mp3tag would no longer disclose the elements of the iTunes files, the titles and art; instead, MP4 is indicated for most files, namely the iTune files. It just seemed to change from one day to the next presenting the id3 tag info and then only "MP4". The information is presented within iTunes (Windows) OK but I've been having trouble losing cover art when syncing the PC to iOS devices so I wanted to ensure all tag elements are intact in the music files.

I found another tag editor, TagScanner, and it reads the MP4 files in their iTunes library folder and indicates which apparently have missing id3 tag elements and lets you retrieve them from Discogs and Amazon like mp3Tag and imbed the info within the MP4 file. I guess now I understand that MP4 are containers that (also) have id3 tag info. Once added to the MP4 files all elements then are viewable within mp3tag (and Windows itunes). However, it is uncertain how a full on sync of 3,000 "restored" files to iPad will work. The iTunes Store may detect a "wrong" tag for purchased iTunes that have been "repaired"'using TagScanner or mp3tag and foul up the library and the sync process.

So, I guess my confusion is having used mp3tag for many hours to clean up MP3 and AAC files and then one day find the iTunes files no longer show their titles and art within mp3tag. Perhaps it was an update to Windows iTunes that did this. I guess I thought that MP3tag editor was supposed to work with MP4 tag info as well. Once the files have been imbedded by this other product they appear like they used to in mp3tag. Is mp3tag supposed to be reading these MP4 files too?

I cannot say anything to the plausibilities of your workflow.
It is well known that iTunes likes to store tag information only in its database instead of writing this information into the files - so perhaps that is one source of the problem.

AFAIK it is possible to force iTunes to write database information to the files by using the function to change the ID3 version - if this also possible for MP4 files, I don't know.
So if iTunes does not store the information in the files, MP3tag can hardly read it.

I would not use iTunes as tagging tool but only MP3tag. Because then you can be sure that the information is written to the files.
Also, I would not allow iTunes to get any tag information on its own. You should be able to control any changes.