I'm like 90% sure the faction quesltines don't intermingle with the main story. I think they push you towards some similar places, but I went through first playthrough beating Ryujin and leaving the Freestar and Crimson Fleet stuff partially done, and I didn't even talk to UC Vanguard. Current playthrough, I've not touched main story and completed Freestar, Crimson Fleet, and UC Vanguard and haven't noticed any interference.