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.
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