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But if we do like it, it means that we have to restart our colonies and that is what is killing me!
Actually you don't! It supports being added to an existing vanilla game. Though of course the progression will be way off.
Adding the DLC to an existing save seems to only add one location for the royal faction, unless a mod I had caused that somehow...?
Yeah, it won't add full settlements since settlements are already generated. The faction will still work fine though.
If I get the DLC, can I choose to not have it activated during a playthrough? Like, if I wanted the vanilla experience again for a new colony, could I disable the DLC?
Absolutely, it's easy to turn on and off.
You can also keep it on but disable royal progression quests (and just keep the Empire faction as a normal faction and keep all the new quest/challenge/implant/research/enemy content).