If you use an internal mount flange on the 4" pipe, you can leave it high then cut it flush with the floor when done. Just make sure it is plumb, or the flange won't sit flat. If you notch the tile first, you won't have to drill holes in the tile to mount the flange to the subflooring.
I'm not sure you're using that fitting properly, though. See what the pros have to say. You may have it in backwards, and for what you want, need a 4x4. You normally don't want to go from a bigger to smaller pipe, but I think there are some exceptions right at the flange...check to be sure.