What is the situation now with the concrete floor/pipe and flange? In many cases the flange is in place when the concrete is poured so there is no choice. A normal flange goes on around the pipe and needs to go down into the concrete around the pipe. Are you using a flange that mounts inside of the pipe? The flange should end up about level with the tile or with the flange sitting on top of the tile. What you don't want it the flange mounted too high and/or not fastened to the slab since connection to the flange is what holds the toilet securely in place. I would second doubling the wax ring with an additional flangeless wax ring or: using a wax ring with compressable foam inside the wax or: using one of the new waxless gasketed rings designed for use with heated floors(wax melts when heated).
