After talking to Uberlord, I've whipped up a really quick patch that allows an arch/subarch module to not set CFLAGS which will just let the CFLAGS from the profile be inherited. This will result in a make.conf that's empty except for the comments, but everyone seems to be okay with this.
Created attachment 118650 [details, diff] something to appease bugzie
This is in SVN.
This is now in catalyst 2.0.5_pre1 and ready for testing.