In my (admittedly limited) experience with buying books from Baen and Fictionwise, their books in Mobi and especially PRC (in Baen's case) are very poorly formatted. While they technically work on the Kindle, they're pretty ugly. (Then again, the same can be said for some of the ones you buy straight from Amazon)
So it really seems like trial and error. Try the Kindle format first, if it's ugly, then try downloading the epub and converting that (though you probably will want to load it up in Sigil first and save, it seems to convert a lot better if you do that, I guess because Calibre can read the TOC built by Sigil better than some of the ones made by other methods)
On the other hand, from Manybooks/Feedbooks just download the kindle format. I haven't really any problems with books from there (just one from Manybooks that didn't have chapter marks, but then it was a novella, not a novel)
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