I just did a test and the pelagos (0.26.4) mod starts up together with mine without issue. I cant tell what could cause your problem since I could not reproduce. Try to update pelagos, maybe that could help.
Soon I will extend the 'compatibility mode' setting of this mod, to not remove rocket turrets and related technology and recipe. I also plan to add an option to opt-out from missile radar coverage, maybe that could help since it looks like the issue has something to do with atomic bomb. so keep an eye out for an update on my side, that may solve the problem - I cant promise it however, because as I state before, I could not reproduce. For me a 'new game' works just fine.