The off-line user manual package (.deb / .rpm ...) does come from the distro repo and that can lag behind installations such as flatpak. At the moment, the only one I know about is Debian 13 which comes with Gimp 3.0.4 I use a 'buntu PPA Gimp 3 and no manual package for that. Your situation is not unique.
You have the source code, so you would have to compile that and still no good for your flatpak. The help files are 99.9% .html but that 0.1% is enough to stop a manual unpack/move working (I have tried it, you might be more successful). It will run on its own though.
Edit: This is what I mean, a Gimp 3 help ( unpacked .deb package) running stand-alone but not from my Gimp 3.0.6 appimage, such is life.
You have the source code, so you would have to compile that and still no good for your flatpak. The help files are 99.9% .html but that 0.1% is enough to stop a manual unpack/move working (I have tried it, you might be more successful). It will run on its own though.
Edit: This is what I mean, a Gimp 3 help ( unpacked .deb package) running stand-alone but not from my Gimp 3.0.6 appimage, such is life.