Yes, I have them both, but I can't tell if they're correctly configured.
In this case, only ~/.fpc.cfg will be read. The correct configuration is a single -Fu that points to your fpc units directory, in this case:
-Fu/home/mati/fpc-3.0.0/lib/fpc/$fpcversion/units/$fpctarget/*
I don't know if that's correct on your machine, it should contain rtl + each individual packages directory, for which the * is for. Right below them, are the .ppu's and .o's. Other than that, everything else is wrong (unless you customize and you know what you customize and how to configure them).