> Flatpak ships as it's own system managing Mesa versions.

Mixing and matching the kernel and userspace mesa components is subject to limitations. However it will transparently fall back to software rendering so you might not notice if you aren't doing anything intensive.

Related, being a container flatpak has no choice but to ship the mesa userspace component. If it didn't nothing would work.

> My understanding with Mesa is that it has very few dependencies

Some of the shader compilers require LLVM which is a giant dependency to say the least. But with Valve's ACO for RADV I think that could technically be omitted.