The cause of the illustrious and inconsistent GC end game freeze bug has been found and fixed thanks to Corey from the EAW X team. The cause was the high AI combat power values of some of our units, which only seemed to cause the freeze at the very lategame when the high tier units were out on the field. This explains why only some people got the problem and others not, and the wildly inconsistent times at which it happened.
This has been fixed now and a final patch containing this fix will go up sometime in the next few weeks. We're working on putting more into the patch than just this, and this will likely be the final patch for a while. Special thanks to Corey for finding and sharing the cause of this issue.