Attaching toilet flange through tile and uncoupling membrane
You should be fine going through the Ditra and tile into the wood. You don't really need to be concerned about the waterproofing under the toilet as it's open around the closet flange anyway. The uncoupling aspect will not be affected. The process of uncoupling is to allow the subfloor to shift without cracking the tile. A few points fastened down won't hurt. If you are still concerned, use a high grade construction adhesive and hope it's not you who works on it next.