Yeah. You'll see patrols of BoS walking around (and their Vertibirds). You'll see RR agents. Even
So yeah, there will be encounters with these groups. Not sure why you wouldn't like it though. It just shows that the group is having more influence thanks to you.
I would have loved to have seen some sign of the MM without my characters input, I had one patrol in 90 + hours of gameplay......this combined with Preston is why the don't exist in my current playthrough.
The further you get into the story, the more of them you'll see as well.. If you get to a certain point with the Bos, almost every time you get into heavy gun fire, they'll drop on your position and "help-out" This can get really annoying during any sort of exploration. I found it best to do all of the world exploration before getting to the point where the Prydwin comes... On that note, I've never seen the Railroad faction outside guarding or doing anything. If you side with them, you obviously wouldn't have to deal with the Bos scumming your xp post end-game.
I dont think the entire faction will turn against you (but I could be wrong). After siding with
I think you're safe as long is there is no 'named' NPC in the group you kill and your current companion isn't part of that group.
Though I'll add I wouldn't bother just killing all your friendly NPC's just because, unless that's just the role-play you are doing. It's always pretty easy to find enemies to kill in FO4. Note however if you are wanting to level up you get a lot more EXP just doing side-quests for factions than from kills.