I just finished a huge game using version 15c where I deliberately avoided numerous opportunities to win by domination because I prefered to win by building the tower of mastery. However, I goofed and accidentally won by domination while trying to get the last free mana on the map in order to create mind mana, which was all I needed to build the tower of alteration (the last tower I needed). Nobody had any mind mana (even after building the wonder to create more mana).
It would be nice if the tower of mastery's entry in the victory status page (or whatever you call that page) helped take care of some of that bookkeeping. Especially since it seems that if I goofed and had a worker convert the last free mana into the wrong type of mana nobody could build the tower of mastery in that game, regardless of what they captured, built or destroyed.
While I obviously made some mistakes, I'm still left with the impression you really have to actively work at avoiding winning via one of the other criteria if you want to build the tower of mastery (unless you go for broke and disable the other ways to win when you start the game). That doesn't seem right. It should be an alternative path, not a second win.