Which files (except the Mozilla Active X) is not arch-neutral? Fonts are, stdole32.tlb (as created by the Codeweavers program) is.
You said it already, Moz AX control isn't. Might as well keep them all in one place.
A virtual Windows drive isn't useful for non-IA32 users anyway, as they can't run just any old Win32 binaries. So it's sort of a moot point ...