Currently we have gentoo-syntax-1.7 in both categories, which will result in a binary package name gentoo-syntax-1.7.tbz2 for both of them. As a workaround, we could use even and odd revision numbers in app-emacs and app-xemacs, respectively. (This would also solve the earlier ChangeLog collision, no more need to rename it.)
Seems this is fixed in Portage, see bug #133908.