The pros here may have a different approach to this, but here's what I'd do. Since you have easy access to the drain line, I'd cut the pipe off and start fresh. This would allow you to make no more hole than necessary in the sub floor and tile and you will be able to position the flange on top of the tiles as recommended. You may want to notch the tile for the screws which should go through the tile and into or through the sub floor. I prefer #12 stainless steel screws for this. The new flange should be one with a stainless steel ring as well.