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.