I agree about the logical gap, but I never understood why, speaking pragmatically, they chose to make synths in the first place. IF they wanted to use the Commonwealth as some giant experimental playground and made synths to be their agents in the field in the wasteland, then they are no better than vault tec and deserve about as much mercy imo. If they did it just to see if they could do it, that is completely idiotic and unethical, or I should say, I never read a terminal or talked to a scientist who indicated they had reservations about trying to make human robots. There wasn't even a benevolent explanation, like making robots to scout that could blend in or something to that effect. They are basically human kidnapping/killing machines and no one apparently cares.
The more time I have to think about it, the more contrived the story endings seem to me. They all seem forced to produce the same type of ending regardless of what you chose, like the developers realized that if the endings were too different, then it might make one more appealing than the other, but then they all end up being the same "hey we have to kill everyone else because they can't exist". It made sense for the BoS because that is their MO, but for the Institute... how many times did Father say he deplored violence before proceeding to kill everything that got in his way? Kid was a dyed in the wool psychopath I know. The Railroad's actions actually make the least sense concerning the BoS. I understand why they destroyed the Institute (that was their goal to begin with) but with the BoS, they are openly retaliating against a group that has a larger presence outside the Commonwealth. As an underground movement, they should have relocated, not made an open conflict with a military-esque organization that has the fire and man power to completely destroy you. I get it, they are an existential threat, but the whole plan was crazy. It worked, but what happens when the rest of the Brotherhood makes their way out west (or east I don't know where they are located at) and starts stomping a--?
I agree though. With more time to think, it isn't that the endings are bittersweet so much as they seem contrived and outright stupid in some cases.