People have talked about this in other threads. It seems bugged. People have lost the game even though the enemy mind flower is in their territory through conquest or destroyed. Also, building +mind flower point buildings seem to be pointless after it's finished. Don't ask about what happens if you capture a city that has +mind flower points but doesn't have the mindflower in its territory. Maybe the universe implodes?
It seems (by reading other people's threads here and on other forums) that the only thing that you can do to stop a transcendence victory is to completely wipe out the other civ. Sure, that defeats the purpose of the idea of putting the mindflower on a tile, but ... that's how it works until they fix it.
There might be a bigger bug at work here, but I haven't read anything about someone bragging about how they sabotaged their rival's mind flower and closed them off from victory ... so ...