Won't work...you'll almost certainly never be able to seat the toilet unless yo uwant to put it on a platform.
You'll need to lower the flange.
Often, older houses with mudbeds can't support a cbu/tile floor; they aren't stiff enough. The mudbed acts like a solid floating floor that holds things intact, but when you remove it and then screw things together, you are at the mercy of the joists and wooden subflooring. You need to determine the stiffness of the floor. If you are going with ceramic, it needs to be at least L/360, stone needs L/720 (twice as stiff) and requires two layers of ply before the cbu.
Check out www.johnbridge.com for tiling help.
Post a picture of the flange you have, and it will be easier to help you fix it.