Not all the maps in the game are the same because not all instances are the same. Not all instances are game generated instances. Some instances are actually created like a SG Base. The one that is most used in the game for example is the Midnighter Club. It's a SG type Base as opposed to being Generated like other instances. As the Devs moved forward from that issue, issue 12 I believe, they made more and more instances like that.
Now saying all of that, I also know that the maps for the SG Base type instances are different then the game generated instance maps. Is this possibly what you are seeing?
The game is Twenty years old. It has new on top of old on top of older code. I was once told the code for CoH is like a Pool of Sewage with a clean bucket of water thrown in. You may just be seeing different code processes from different time periods.