I'd be particularly interested to know if learning something like Template::Toolkit or other general purpose tools might allow me to intelligently handle updating config files in general.

Template Toolkit is precisely what I use when building Apache config files from within Perl. IMHO it is worth the (not inconsiderable) time required to learn it as it is so flexible you will subsequently find it useful for all manner of other scenarios.

Conversely for parsing the config files I recommend Apache::Admin::Config which seems to work reasonably well in most cases.