I think I found a bug in the GCC makefile exported from Studio. Either that or I'm doing something stupid. I guess the chances are 50-50 :)
I made a project that has source files from multiple folders. I exported the makefile. It wouldn't build. I believe it couldn't find the source files.
I then specified the source file folders with VPATH. Now it works like a charm.
It seems Studio should include the VPATH in the makefile. If it seems that way to others, I suggest Atmel include VPATH when generating a makefile that contains files that aren't in the project folder.