perhaps there is/was just a rush of undies-on-the-outside fetish artists running the comic book industry for a while. i mean, even if we ignore the x-dudes, there's certain incarnations of superman, batman, aquaman, etc that also have the undies on the outside look.

as for beast, i suspect the idea is to show as much of the 'beasty' side as possible (see? he's TOTALLY covered with fur, not just his face/hands/arms), but not allowing him to be totally naked, presumably for the sake of not having to totally neuter him and/or invite protests from parents (you can see this also in some versions of fantastic four's the thing).

ya know... off the top of my head, i can't think of any villains who wear their undies on the outside. maybe if they did it would trick the heroes. 'oh wait! he wears his underwear on the outside! whew, he must be a hero like us! i guess those must be bad guys he keeps killing! Let's go help!'