Closet flanges should always have the bottom of the flange resting on top of the finished floor. So to answer this specific question, the tile should be under the flange and the flange should be secured to the subfloor.
If the floor finish in the room that the closet opens from is tile, and the base of the closet is at floor level, having the same floor finish in the closet is attractive and makes it easy to clean.
The toilet should sit on top of the new tile.
this
With a deep floor flange Or a wax seal with a horn and extra long Brass floor flange bolts
what is the waste allowance with floor tile
tile should slope sightly down toward the drain and drain should be recessed slightly below the top of the tile
Pull the toilet. Check the closet flange. If it is not loose or broken, replace the wax ring and closet bolts. Reset toilet. Level with wobble wedges. Caulk base of toilet.
yes the tile has to be fixtures and then put the tile
Yes, if you want uneven and broken tile. You should level the floor first.
Extend the Wax Ring instead. The Fluidmaster No.35B Wax Extender Kit is specifically designed for problem areas where the floor flange is 1/4" to 1" below the surface as in tile work. The cost is under $6. Some plumbing supply stores sell an extension that bolts to your existing flange. If you need an extension due to new tile work, this will do the trick. If the flange is only one quarter inch or less below floor level, you can just use two wax rings.
Depends on how much you need. Sometimes you can just use two wax rings. If that doesn't do it, you can use a PVC toilet flange and use it to make up the difference. Cut it off the right height and use a wax ring between it and the old flange. You cut the old flange out and extend the pipe and a new flange. If you put backer board down first and then the tile, you probably raised the floor level about 3/4 of an inch. Two wax rings with the black funnel insert in them should be enough to seal the toilet to the drain.
Wonder board.