I strongly recommend to regen them on the build process.
No, because the makefiles need to be regenerated using an
fpcmake built from the up to date version. So there would be the problem that this would need to be built first, but that might depend on code only available in the up to date RTL. So you'd have to rebuilt everything anyway.
now after every fork update I have to rebuild all makefiles and push a new, only with the makefiles, commit to merge 
That's simply how it is when you have a pending change for the template.