Most professional tile setters will tile to the pipe, then the toilet flange/wax ring go on over the tile. The tiles that the toilet will placed on really needs to be as level as possible. For tile, the floor should be no more than 1/4" in ten feet out of level. Most regular thin set can be built up to 1/2 inch or so.
If you don't have enogh fun doing the bathroom, come out here I'll gladly let you set all the tile you like.

ROCK 'N' HAXIOM Theater