Yes. I've several installations of perl on my system (ranging from 5.005_04 to 5.14.2), and each version I've build using different options.

I typically use a different directory for each versions, but several builds (with different parameters) will happely live together in the same directory. I usually build my perls with and without threading, with 32 bit integers and with 64 bit integers and with debugging or no debugging support. That is, for many versions of perl, I have 8 different builds. I do rename the binaries though (so I have "perl32", "perl64", "perl32thr", "perl64thr", "perl32-d", "perl64-d", "perl32thr-d", and "perl64thr-d") foreach version.