The flange should me mounted over the tile and the flange needs to be bolted down.
First, without bolting the flange down, you create a situation where the toilet will not be bolted down properly either.
Toilet bolts are held firmly in place by the flange. If the flange is not securely bolted to the floor, the toilet will wobble and tend to leak no matter what you do.
Second, a flange is designed to be placed on top of the finished floor. Not placing the flange on top of the finished floor only leaves open the greater possiblility of eventual leakage.