I always use Html files as source files myself. But I am coming from a different point of view as I do (or rather did) first and foremost Mobi books. And you are perfectly right: <pre> is not very well supported at all by mobi. I make my htmls as simple as possible, using mostly only header and paragraph texts. If I need special formatting, I use breaks, aligns, bigger and smaller fonts. These 3 work fine with all formats and keep it simple.
I avoid BD for the same reason Nick does. BD tends to play around with my perfectly good HTML code.
I used to create a mobi file first and then LRF and IMP by importing that PRC file into Calibre and Mobi2IMP. I have changed that method somewhat now by using my HTML source file with Calibre and thus creating LRF and Epub, because epubs are easier and better to create that way.