This is a very dumb question that will probably undermine my integrity as a speedrunner, but since there is a way to get to the final bowser fight without going through the Bowser 3 Level in Version 1.2, would it be allowed to get 90 stars in the game regardless of whether you unlocked the third overworld and then get to the fight that way?

Nope, not allowed. The point of the category is to reach the final bowser with the (original) intended star count without the use of the pipe. However if you were to run 0 and 160 star feel free to use the pipe.