I can't tell you a while lot about the technical side if it. Definitely M3U playlists are strictly text files that contain the exact file path of the tracks, including file extension. For MusicBee's MBP playlists, I'm not sure what all is happening in the file except that it allows more custom settings in MusicBee.
Regarding this, though:
Re your suggestion of generating playlists from tags, I don't think that would work for me as all of mine are 'hand-curated', i.e. I select individual tracks to put together, rather than some theme or something based on a genre or any other tags. And anyway, my request is more about ongoing maintenance of existing playlists (I have many!), than making new ones.
This is exactly what my suggestion would help with. Rather than "curating" by adding tracks to a playlist, you would curate by adding a custom tag to the track, which MusicBee would then use to assign it to the playlist.
This allows 100% transferability between files, because all you have to do is copy the tags from your original file to the new one and the playlist will be updated (you can copy in bulk using the Additional Tagging & reporting tools plugin). Like I said, if you add file type to the playlist criteria, then you won't even have to worry about removing the mp3s. You can either have a second FLAC playlist or convert the original.
This will make ongoing maintenance much easier on you because once it's set up you don't have to mess with the playlists, they'll take care of themselves. And you can always export them to static playlists as needed.
For example, in my library I have a custom tag called Playlist Filters. The values I use include "Dance" (songs I like to dance to), "Bond" (James Bond themes), "Poem" (songs based on poems), "Local" (local artists), and "Wing by Wing" (a playlist from my cousin's wedding).