From this updated comment: "... I don't have web admin rights and I don't want them .."

I think that the answer is quite clear. You don't want mod_perl.

"Are there any other reasons that you might choose one exclusively over the other?"

Yes. If i have root access, and plan on coding up a fair sized web app, i will choose mod_perl. If it's just for an example, then i choose CGI.pm (well, to be technically correct, plain jane Apache). If i don't have root access, such as my perlmonk.org account, then i don't bother with mod_perl at all.

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)