it should be fairly easy to patch Config.pm and Config_heavy.pl to just set the library paths similarly by looking relative to $^XI've done that a few times myself. It is, as you suggest, just a matter of hunting through Config.pm and Config_heavy.pl and replacing every occurrence of C:\original\location with D:\new\location (or whatever). Doing it manually (which is the only way I've ever done it) is a little tedious, but only takes a few minutes. As you've noted, @INC is self-adjusting, so there's no problem in that regard.
Cheers,
Rob
Update: Ooops ... I now think xdg might have been suggesting something else than merely editing Config.pm and Config_heavy.pl.