Wood – How to anchor floating toilet flange

There isn't much allowance for raised flanges in most US toilets I've seen. The critical feature is how much higher the under toilet "ceiling" is than the bottom perimeter base that sits on the finished floor. Since this dimension is intended to work with a standard wax ring, there's little chance a 3/4" protrusion will work. Not only do you need physical clearance between the flange and the "ceiling", there also must be room for the wax sealing ring.

The other potential conflict is the outlet horn and how it fits into the small bevel of the flange fitting. Again, there needs to be room for the wax to fill this gap. You do not want any direct physical contact between the flange and horn.

Simply supporting the flange is not enough. The perimeter base must be fully supported. If you try to install the toilet as things are, the toilet will be balanced on the wax ring. It will wobble every time it is sat upon, eventually forcing all the wax out until the "ceiling" is bearing directly in the flange. While the wobble will diminish at this point, it will still wobble. The seal would obviously be compromised.

Whatever you do, the perimeter base must be solidly supported. The obvious solution is lower the flange, though very difficult in your case. Another solution would be to raise the floor, which I imagine would be undesirable. The only other possible solution would be to raise the support of only the toilet base, such as setting it on a grout bed. Depending on the nature of your flooring and the actual final thickness of the grout, this may not be too bad a solution. You would need to spend enough time finishing the exposed grout around the toilet base so that it is smooth and easy to clean.

I would not leave a gap, and use screws long enough to reach through the plywood through the backer board. Make sure the flange is well supported or you'll have problems with it down the road if not immediately.

Maybe an even better solution would be to have plywood of the right thickness span the gap between the subfloor and the flange, and still use longer screws that will reach the subfloor. Cement backer board tends to be weak at its edges and may not provide the support the flange needs. Plywood on the other hand is very strong at its edges and should hold up marvelously. This small piece of plywood can be kept inside the area that the toilet bowl covers so you won't have to put tiles over it or anything. You might want some plastic shims on hand for the job too, in case the plywood and flange don't meet nicely. Good luck.