Your solution works fine with VLC and videos should be played with that specialized application.
Stopping:
Stopping does not work, sometimes gets me two VLC processes. MB does not react on stopping or closing VLC. And stopping in MB does not have impact on VLC.
Tagging:
I have different music videos (mp4/mv4) of concerts with each containing serveral titels/tracks.
I tested around an saw, that mp4-tags are not read by MB.
If I have an similar mp3-file I put an cue sheet aside and can handle these tracks just as if they were single files.
Together with cue sheet files aside an m4v this also works within MB, except that the video always starts at the beginning.
I would appreciate when you add a start time to your interface to VLC, and probably also a play length. I know that VLC can do at least start times.
I know that VLC also writes XSPF-Files with bookmarks, but that is a different story and a less easy editing variant to cue sheets.