I believe that *.alias files (which include /usr/X11R6/lib/X11/locale/locale.alias and /usr/X11R6/lib/X11/fonts/*/fonts.alias ) should be %config files so that when people add their own aliases, they would survive the upgrade. I am not sure if *.dir files should be %config files, but it may also be reasonable - so that people could add extra fonts/extra locales/etc and still survive an upgrade.
This has been assigned to a develope for further review.
While I agree with the motivations behind this, issues in RPM packaging make it QUITE DIFFICULT to do "right". Chances are we won't see this happen in any errata releases for 5.x, but 6.0 should fix the problem, as well as rebuild the fonts.dir file on the fly whenever a new font RPM is installed which adds/removes fonts from an existing font directory.