I didn't mention this last night (probably because I was EXTREMELY tired), but the entire gentoo-x86 tree has been converted to the virtual (YAAAAYYYY!!! *kermitflail*). As long as you don't use any overlays, you should now be able to switch your pkgconfig implementation to pkgconf[pkg-config] or pkg-config-lite with no problems.
Please give them (mainly pkgconf) a try and see if everything works. :D
