Even the large continental colonies probably need a certain amount of help with humans transporting new queens/males from one side of the colony to another side to help keep the genes similar. It's not like colonies that large only have a single queen. And with a large number of queens there is the possibility of genetic divergence from each other.

Unless the ants in those colonies have developed some sort of system themselves where they distribute new queens/males from one part of the colony to another... but I can't imagine that it would be easy for them to transport breeding ants (or for those ants to fly for that matter) 900km from one side of the colony to the other.

On the other hand, when it's time to mate, all the breeding/flying ants take to the sky. It's possible that each of the points of exit is close enough to other points of exit that somehow genetic 'stability' is maintained through this mingling. It just seems incredible that just random chance and proximity of flying/breeding ants to others with the beginnings of genetic divergence are able to keep genetic divergence in check to a degree that allows for these HUGE colonies to maintain close enough familial ties to cooperate.

Edit: Sorry, this just kind of turned into me rambling on with your post as a starting point.