I've played through the game twice now. The first time was before the patch. This time with the patch. The first time through I got a prompt when a choice would make me hostile to another faction. This time I never saw these prompts. The flow of content seemed a bit different as well, which allowed me to fully explore a companion's story that I missed the first play through.

Were these changes really made? It seems kinda odd.

No. I don't think the patch changed the .esm at all.

Perhaps a mod removed the prompts.

Only prompt I ever got was about the BoS hating me if I did Mass Fusion