Unofficial Fallout 4 Patch

Random encounters will not be started when there are too many actors in the loaded area. If you develop the Starlight Drive-In settlement beyond a certain settler count, REs at that spot below the bridge will stop occurring - no matter whcih RE was the last one to occur there.

This is apparently handled at engine level: the RE zone triggers still send story events, but the story manager will not process them, without throwing an error.

NOTE: Removing the cooldown timers on RE zones is not recommended as it will increase your chances for getting random CTDs quite considerably. The engine doesn't like it if there are too many actors in the loaded area, and this is not getting better by just running the game on a fast PC with tons of RAM.

I did some experiments with the game myself and found down that those bodies are container of random quest note, usually seeking something in a place. As long as I don't finish that misc quest, the body will not cleaned out. However does that quest system work like that? Preventing any random encounter from spawning until completing the quest.

Yes, that's possible - BUT this type of encounter does not block the trigger.
If an RE trigger starts a treasure hunt quest, it technically first starts the treasure hunt master quest. That quest places a dummy (invisible) for the trigger to look for and subsequently starts the actual treasure hunt quest which it controls on its own. The dummy runs a script that reactivates the trigger and cleans itself up when the area unloads.

Yeah I notice at some area that doesn't block further RE, but the dummy didn't clean up. It is still visible as long as the quest remain active.

???
You can't see the dummy. It's a marker object.

My mistake, it is the corpse containing the quest giver note.

That's perfectly normal as long as the treasure hunt quest is still active because it is in a quest alias and this prevents it from getting cleaned up. Once you have the quest done, it will disappear.

Closing this as invalid because the initial claim of a random encounter quest blocking the trigger is false.

Why some triggers may stop spawning encounters is another question that may need further attention, but I doubt that we can do anything about it. Triggers do in fact fail occasionally to start an encounter and there are no papyrus errors thrown. Once this happens, RETriggerScript will send a warning through game script (i.e. this message will appear on the papyrus log, even if the script has not been compiled in debug mode) which reads: "Failed to start a random encounter. Check number of actors loaded in this area, and number of REs currently running." Note that this is the wording on the vanilla script and, so to say, a message by the devs. It also provides the best lead to what is happening: apparently, the story manager will not start any quests if there are too many actors in the loaded area. This is supported by my own observation that the trigger under the bridge near Starlight Drive-In stops to spawn anything once the workshop has grown beyond a certain settler count.