The standing advice about mod_perl and threads from the mod_perl community is to not use them if you have a choice. People on Windows have to use them, but on Linux you're better off using the prefork model. It actually uses less memory than the threaded model and avoids problems with CPAN modules that aren't threadsafe.

Regarding the VirtualHost issue you mention, this is a pretty basic limitation of Perl: you can't run two different versions of the same module in one interpreter.