I know you can stop the upgrade of ALL designs, but I thought I could just prevent a few things. In the design screen there is a "Default Retrofit Stance" I changed it from auto, and figured that would be the end of that. Sometime later sure enough there was a new design. Now being as the stations/ships themselves don't retofit the actual object unless I do it, I'm a bit confused. A broken feature? Something that was overridden by another choice elsewhere?
Why do I care? Well I'm starting a game, with zero pirates, zero other colonies, return on the Shakturi type scenario. The background for my little play thing is that the Shakturi wiped out all the other races, the only race left in the entire galaxy is my race, plus whatever other races stuck on backward planets. Now I need to rebuild my empire and crush the Shakturi upon their return (which luckily I can control since I don't have any pesky AI civilizations uncovering things that should not be explored!)
However I've noticed a problem early on, is that I can literally get stuck with not enough resources. And since there's no smugglers (pirates) and no one to trade with, there's no way to advance. I thought I could freeze the design and simply make it a stripped down version of mining/research stations (no worries about them getting blown up after all!) and go from there, but nope they changed on me. I got around this by not having the designs upgraded until I was sure I had supplies for everything that was necessary, but still it was a bit of a pain.