theme sensitive color schemes that need to be addressed for such an endeavour...

This can be addressed by doing the coloring in CSS; post processing (using the Syntax::Highlight::Perl keywords for classes):

Then everything is still black unless you have a style sheet with code.perl > .Directive { ... } etc. and each style could have its own code styles companion.

As much as I'd like to see it, it does seem like a big headache, it would mostly only improve readability of longer code, and even using the faster methods available, it would slow things down a bit.

Oh, and this node, already listed below by cchampion doesn't mention that Perl::Tidy is customizable with its "formatter" arg to perltidy() though it's difficult to use.