Probably a bug. I've noticed other wikis also accepting .mp4, I have no way to check but I doubt they always have. Also enwiki, it didn't have any mp4 files yet but it does now: https://en.wikipedia.org/wiki/File:Yermi.mp4.
Yep, that's a regression in the extension.json migration. The addition of file types to $wgFileExtensions was being done twice, both in the extension.json and then again dynamically, causing the way that 'mp4' was removed from the list to fail because it only removed one instance of it.
Scheduling the fix to go out tomorrow morning pacific.
@brion Perhaps they should be left up for a while. They seem to trigger strange bugs. For example https://commons.wikimedia.org/wiki/File:Maalwerk_Volmolen_Frankenhof.mp4 which is a video that was shot in portrait mode, gets completely messed up when wiki makes vp9 out of it.
Should I file bug reports for such glitches or not as uploading mp4 should have never been possible in the first place?
Update: reported as T209560
Yeah, file bug(s) please as appropriate.
TMH can/does/will support MP4, but just because Commons isn't allowing it, doesn't mean it's not a valid bug in one form or another, and therefore other users of TMH may benefit :)