Yet another manafestation of TIMTOWTDI. The fault isn't with POD, which is just a form of mark up, but with inconsistency with its use. You can't avoid people using the richness that is provided in ways you didn't anticipate; that's what people do.
Changing from one type of markup to another doesn't solve the fundamental problem, and in the case of POD to XML, probably makes it worse!
Remember the context for POD. It is to help provide documentation in the source, so any markup that is used to manage formatting in some other context has to be pretty light weight or the documentation just doesn't fit with being in the source in the first place.
Probably the only solution is to provide a good set of guidelines for the use of POD (or whatever markup may be used) so that both usage and apperance are consistent.
Perl is Huffman encoded by design.