I am replacing a linoleum floor with tile and needed to replace the existing toilet flange, due to a small leak and corrosion of the flange. Since I have the ability to raise the elevation of the drain (if needed) would it be best to set the flange on top of the tile or is it standard to set it on the cement board? My tile and flange are both 1/4" so the flange would be flush with the tile floor surface. Would putting a double wax ring or flange extension be a good idea if it were set on the cement board?
I am concerned with cracking the tile when drilling for the screws that secure the flange to the floor in case this is the preferred arrangement.
A toilet flange should be installed on top of the finished floor level...on top of the tile in this case...with only the thickness of the flange above finished floor level.
To keep from damaging the tile, tap a starter point with an awl to help prevent the masonry drillbit from skipping.
Solidly bolt the flange to the floor, level the toilet (a level across the bowl) with beveled plastic shims made for the purpose if necessary, and securely bolt the toilet to the flange. A single wax ring is all that is necessary. Don't overtighten the toilet bolts or it may crack the base. Just snug them enough to prevent any movement of the toilet.
Use a bead of anti-mildew tub-and-tile caulk around the base at the floor, except in the back for easier leak detection.