I think the focus is the dog. I restarted, went straight to Goodneighbor (which wasn't an easy trip at that level). Did the Memory Lounge (saw Deacon in a pod too), met the vault-tech ghoul, then went back and saved Preston, Mama, and the rest. Then avoided Dogmeat, and met them in Sanctuary. And frankly, the story made more more sense. Everything seemed to fit.
I still haven't met Dogmeat. I'll help out the BoS for a bit, then go save Nick and take it from there.
The dialog, story- it all makes sense now. Even the lady at the lounge - at first I never knew why she was there. Now I know.
I think you are right, at the least minute, they changed the beginning. I don't know why, but it looks like they did so that you could meet Dogmeat, and get the PA right from the start.