Already done flatpak config for Dwarf Fortress as part of my testing, so setting it up for OpenMW as well shouldn't be impossible.
Edit:
There we go, that wasn't too hard. Only took ~3 hours of writing, compiling, and repeating.

Still need to trim away lots of useless content, but the game builds, gets correctly packaged, and it runs fine on my Intel/NVidia laptop.
Once it's trimmed down to a more reasonable size, I'm going to look at publishing it on flathub, so it's easy to install for all flatpak users.
Doing the work on my flatpak branch, if anyone's interested.