Use MACHINE_ARCH instead of TARGET_ARCH

TARGET_ARCH is only for use in Makefile.inc1 contexts. MACHINE_ARCH is the
preferred thing to set. Makefile.inc1 sets MACHINE_ARCH in the cross build
case, and make sets it in the native build case. This will fix anybody doing a
native build. Add a comment for why we have to do this dance so when/if the
problem with CFLAGS is fixed for the kernel this workaround can be removed.