Dumb questions:
(1) You're moving the wall: which one? The one that the water supply should have been in? If so, then don't you need to move the pipe to which the flange will attach so you have a 12" rough-in from the finished wall? If you're moving the closet bend, then the pipe and flange can be planned to be at the right height. Presumably, a professional would do this work as well.
(2) If you were just going to install a new toilet, I'm not sure what looks so horrible. Yeah, it's below the finished floor, but it doesn't seem like by much. It seems accessible. It has extra crud on it which all needs to be cleaned off so we can see the actual flange, and the slots need to be cleaned out and exposed. But unless I am missing something, it's not exactly unusual to find pretty much this situation. I know that Terry has recommended that one just use two wax rings where the flange is below the finished floor, so it's not an uncommon occurrance and it has an easy fix. What am I missing? (Obviously, one would do it correctly if one were ripping up the floor and the subfloor anyway.) Also, while tiling to the toilet is stupid, wouldn't an elongated Drake or something have a big enough base to cover the tile that is there? (Purely academic as the ex-husband's work is obviously all going in the dumpster. That's gotta be satisfying (and unifying).)