It might seem strange, but Smashwords themselves - I find - are very good to deal with. Maybe not the speediest, but they respond faster than I ever got with BookBaby.
The slightly odd distinctions between the old Word way, and the new epub way are mostly historic (as far as I can tell) ... and, sadly, Smashwords don't seem in a hurry to improve their epub support. I assume that's because the majority of people using them are still happy to submit Word docs and let the meatgrinder do the conversions for them. The results are generally usable, if not pretty when you look at the internals.
I've yet to go through the Word thing - I have not done so with my novels. I thought I might give it a try with one or two shorts, and if it turns out well enough then maybe I'll put my novels through the meatgrinder for everything but epub (for the reasons cited above).
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