Great or not great, they are still choices.
If you choose to run those quests on reaper when you know that this can happen, that is your choice. Complaining about it after the fact when you went into it knowing the risks isn't really going to accomplish much. IMO, YMMV.
This isn't anyone asking you to accept the bugs, this is me telling you that if you know that these bugs exist and yet still choose to subject yourself to the chance that they will occur that my sympathy is less than it would be otherwise.
Would it be great if the devs spent many hours coding around fringe cases so that no reapers could spawn behind a locked door/in a cage/under the ground/whatever? Sure, that would be fantastic!
Will this ever happen? You know the answer to that already, don't you?
And since I know that you know the answer, I have to ask, what is the point of this thread? Because "Fix Fear Reapers" is never going to happen, not in the way that you are asking for where they remain essentially the same but many hours are spent coding against the fringe cases you have outlined. And you knew that before you opened this thread.