Different tag types

I've been ripping my new set of Doctor Who blurays. I rip them with MakeMKV and then run them through Handbrake with the Apple 720p-30 factory preset.
When I tag them with MP3Tag, some show up as "MP4 (MP4)" and others as "MP4 (Nero MP4). The Nero MP4 will accept leading 0 for Track, TVSeason and TVEpisode but the MP4 ones will not.

It looks like all of the MP4 ones are 480 and all of the Nero MP4 are 720p but they come from the same original disc.

Yes, this is so. MP4 saves a real number whereas in MP3 files it is a "numerical" string.

MP3tag has no influence on the audio or video data and its encoding parameters. So you would have to check your encoding process.

I wasn't clear or providing complete information.
PRIOR to making any tagging changes ALL of the videos are "MP4 (MP4)"
AFTER modifying the tags with MP3Tag, small files are still "MP4 (MP4)" and large files are "MP4 (MP4 Nero)"
I just tested this with a 720p movie, a DVD movie and a DVD short.

See here: