I expect it's a matter of limited resources. Good as the converters available are (particularly the ones in libprs500) they still take time to use. I get the impression that Baen's e-book department is rather small, and there are a lot of books that would have to be converted. Sure Fictionwise has done their multiformat books, but Baen's folks may not have realized that yet, and may still consider it too big a job to undertake in the short term. Especially when RTF works pretty well on the PRS line.
The Kindle thing is a different animal, since Kindle handles unlocked mobi files just fine, all they had to do was relabel the files they already had and they were done. I wouldn't be surprised if that only took a few hours.