and all that seems to be working as I expect.

We have very different meanings for "seems to be working"!

Perl has no control over how Apache sets up environment variables. That is a problem with Apache, mod_rewrite or your mod_rewrite command.

If you're asking for help to fix this, look elsewhere. This is not an Apache or mod_rewrite support site.

If you're asking for help avoiding mod_rewrite, it would help if you tell us what is it that mod_rewrite does that you want Perl to do.