Never thought that someone would insist to preserve his system ids when site renamed...
Anyways, links maybe are easy to navigate for a user, but adds bunch of problems since every service should be dealing with soft links instead of real locations. In addition chroot and other security related tasks may become very difficult to implement due to symlinking.
There is even a confusion in one single apache vhosts file.
Can you please specify what modules/plugins are actually affected by that behavior? I am thinking of making that behavior as optional.
BTW: Don't bite me if I am expressing new and maybe extremal ideas :-) I just want ISPC to suit my (and hopely other's) needs.