I wish I knew for certain whether all quest givers are only Essential up until you either finish or fail their quest(s). Also whether companions/potential companions are essential only until you do something to make them hostile.
I can understand the use of "Essential" NPCs, but I cannot say I like it as a player nor that I think it is best choice. I guess it boils down to how many complaints they'd get if all currently Essentials were set to Protected versus how many they get now.
Not that I like to go around killing everyone, but I find the fact that you CANNOT kill certain individuals at certain points in the game to be tremendously immersion breaking, and as many have said, it stands as a serious impediment to an "evil playthrough."
So far the "testing" I've done has been quite limited and only done in a few impulsive instances, for example:
1. Something about Deacon just rubbed me the WRONG way and on the way to finish that first mission with him I resolved to kill him, and destroy the Railroad and forego whatever errands they might send me on. Not happening at that point anyway. Now that he is my "follower" (and sent to live with Danse and Hancock at the Slog) I haven't bothered to check if he is still Essential.
2. Danse: I don't think I ever met an NPC I wanted to shoot in the face more than him. Also a no go, at least up through that first ArcJet Quest.
3. Tommy Longegan: cannot be killed, at least not immediately after he "sells" Cait to you . . .
4. Preston and Piper cannot be killed, either before, during or after they are your companion.
5. Virgil: I stole some of his crap, his Protectron got hostile, as did he, but he is Essential still *sigh*
Is there any real reason why every NPC that has the "Essential" flag couldn't be downgraded to "Protected?"
Might it even be possible to enjoy the game if Companions were more or less completely mortal (albeit with perhaps a tad bit of extra damage resistance when their health gets low??).
Thankfully: Maxson !CAN! be killed almost from the moment you meet him (well you do maybe have to endure that little speech of his first). It seems that, irrespective of stealth, this automatically makes the entire BoS immediately and irretreviably hostile, and not sure if Danse stays Essential or not. I fought my way through the Prydwen for quite a while and I think it might have been Danse who finally did me in . . .
Haven't even tried with Railroaders (other than Deacon, who is no longer a RR, and is now one of my lackeys = one less gun to face when I take out the RR).
So when is it "SAFE" to basically try to destroy each of these factions?
1. BoS: you can obviously take them on as soon as you get to the Prydwen, which is refreshing that you can take advantage of their utter stupidity by bringing someone they barely know into their esteemed leaders midst and assassinate him forthwith, but still frankly a bit lame, in that you have to FIRST do a mission with them before you get the opportunity to aggress them 'effectively.' If you attempt to kill Danse and the others on sight in Cambridge, you'd probably kill Haylen and Rhys but Danse of course would be Essential I guess. I've even noticed that sometimes a named NPC who is essential can revert back from hostile because you attacked them to "meh, whatever, we're on speaking terms again."
2. RR: can you just bust in there and kill everyone? Just skip over every thing involved in that faction and just kill every single one of them?
3. Institute. Father definitely deserves a bullet in the head, but while I was there, I didn't try. I kinda wanted to have the freedom to see what this "Institute" was all about first. But it makes me wonder, now that I have the chip to transport back in there (and have yet to piss them off enough, despite having bagged half a dozen coursers out in the Wasteland so far) can I just go back and kill everyone?