I recently did my bathroom floor in 18" travertine. I put in about 300 screws to hold each of the 4" x 7/8" tongue-in-groove pine boards to each the joists, then I put 1/4" hardibacker with thinset and about 300 more screws. I took your advice and used short screws when putting down the hardibacker. It's amazing how much more solid the floor was after screwing it down carefully. Anyway, what I've never figured out is how to make sure the hardibacker is 100% flat. I now have some edges up between the tiles, not too much but still enough to notice.
Steve
Also, by the way, I wound up with a store credit for $785 at Saltillo, which I'd like to get rid of. If you would like a free $75 discount then see details in "Classifieds" posting or call me at 416 536-3340.