The file features/win32/default_pre.prf has rtti_off set by default. How can I change this behaviour from my project file? The .prf file seems to overwrite anything I put there.
As long as you set things after the .prf files have been processed your .pro file should override them. It can be tricky though since in some cases a .pro file can be processed up to 3 times by qmake.
As a last resort you could just edit the .prf file in question.