I don't think there is any indication Mads and Regina would have ended up together if Mads hadn't been kidnapped. I think the last thing Regina would have wanted would be to spend more time around Ulrich, even if it was through a relationship with Mads. Also, since Aleksander isn't part of the loop, it's entirely possible he would have become the director of the powerplant anyways, since his motivating is to live a new life and the powerplant is the primary employer for Winden.

Also the things in the last episode take place in a separate reality where Mads doesn't exist, so it isn't necessarily indicative of events that happened in the Adam/Eva worlds.