It sounds like you're saying that you call exit() just as a short-circuit to avoid running some of your own code that would otherwise run. It doesn't skip any apache phases, so I assume that's all it's doing for you. You could get a similar effect by using exceptions and an eval block.

IIRC, Apache::exit is not supposed to log an error, but that may have changed at some point. If you want the details, the best place to ask is the mod_perl list.