:This is not that hard! Finish the floor job completely. Then install the flange unit so that it is seated right down on top of the tile. Yes, the surface that the wax actually contacts will be 1/4 or so higher, depending on what flange you use.
If it is more convenient to install the flange before tiling the floor, rough it in with scraps of the wonder board if used and pieces of tile, with some cardboard shims to approximate mortar thicknesses. Keep in mind that for the toilet to be properly secured, the flange itself must be securely screwed down to the subfloor (screws through the tile.)