I understand that the toilet flange should sit on the finished floor. I've got porcelain tile on top of a Ditra uncoupling membrane for waterproofing. To attach the flange securely to the sub-floor, I would have to screw through both the tile and the waterproofing membrane, which would seem to defeat the purpose of the membrane. Is there another method for attaching the toilet flange when using an uncoupling/waterproofing 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.
A few points .... Not sure why you need waterproofing under a toilet bowl. Also, you could add an extension flange on to the existing sunken flange. Or, remove the existing flange and add a coupling and then a flange. Cutting out the old flange is tricky. It is usually done from inside the drain pipe with an internal pipe cutter. Otherwise, you may be able to simply and an extension flange ring on top of the existing flange. They come in various thicknesses, depending on the thickness of the tile and grout, subfloor, etc. Yours is a common problem, especially when tile flooring is added afterwards. There are a lot of solutions out there for this problem.