Fallout – Will the actions still affect the companion’s relationship even if they’re far away

The Battle of Bunker Hill is a quest that is given to you by the Institute, which is why they weren't interested in being warned - it was their mission.

The reason you're allowed to inform other sides is because you'll always get this mission regardless of faction allegiance however if you're working for the Railroad they'll want informing because the synths you've been sent to kill by the SRB are in the process of being "saved"/smuggled out of the Commonwealth by the Railroad.

If you're aligned with the Brotherhood of Steel and warn them, then they'll request that you kill the synths.

At this point in the game it is possible to still be on friendly terms with every faction, if this is the case you can turn up to this mission and walk through multiple opposing factions trying to kill each other, with all of them acknowledging you as on their side.

In my experience if you plant something near the bugged plant, assign a settler to that plant, and let the farming run its course, these issues tend to resolve themselves over time.

I've had invasions occur ON my farm plots, and have watched my missile turrets decimate the farm plots, and then not be able to select the destroyed crops.. Poor farm/defense layout aside, this is the circumstance in which I came back later and notice that the plants were eventually revived.

In short, I wouldn't worry so much about micro-managing the efficiency of every single plant. If food and water is sufficient for stability or growth, that's good enough for me!