I am building a new home and doing some of the work myself, particularly the tile in the bathroom. During the plumbing rough-in, my plumber connected the toilet flange. When I tiled the floor, I raised the flange enough to allow the backerboard and tile to slip under it. The flange now sits on top of the tiled floor. My builder noticed it and commented that he would have left it on the subfloor. My question is whether it matters or not if the flange sits on top of the tile or if it would be better if it sits on the subfloor with the tile installed around it.
It belongs on top of the tile. It is when it is on the subfloor that you have problems. If that had been done, you could have needed longer bolts, thicker wax rings, and the seal would have been less secure. You did good.