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Trying to understand conflicts. I have no idea whether this is safe to ignore, or if I should change the load order to make ASE come first, and if I do, does that mean Clean and Simple determines the boundaries? 

It's not safe to do that in an ongoing game, and it is real pain to try and start a new game, jump to the settlement and try to see if the boundaries are extended, or if some new horror of crashing is now resulting.