Hi Scott,
If my training serves me, no worries about the Ditra seams. One of the beauties of the system is the ability to piece all scraps in with no waste. You are correct about the consistency being wetter for applying it to the subfloor, but you still want the mortar to hold a notch. As for above, flat troweling in all directions should fill the waffles well, you need the thinset on top to support the weight of the tile (not real runny). I assume you ran your joists through the Deflecto?
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Brad

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