There's a few things that have to happen (and it helps if you understand how the FO3 game engine works).
- The scavenger will likely not show up in Big Town, until after you run across him at one of the random encounter locations. Meaning that you have to visit one of the random encounter cells, the RNG has to pick that particular encounter, and then you have to wait a few game days for him to finally show up in Big Town.
- Shorty's timer starts the moment that you enter the basemant, or maybe when you get closer so you can hear the conversation. When you get within trigger range, Shorty and the super mutant will start a scripted conversation. If you wait too long, the SM will decide that he's too hungry to wait and will proceed to attack Shorty. If you're quick and have good firepower, you can still kill the SM before he completely kills Shorty.
- As for Big Town, if you get close enough to spawn the cell, then it's possible that there's a timer that starts running. If you never go to the area near Big Town, that cell never spawns, the inhabitants never enter the game... and nothing can happen.
Your first point about the scavenger is interesting.
Your info on Shorty is right on the money and another thing is if you open the cells from the other floor in the jail (terminal) a cockroach could kill Red and I've had that happen to me. For that reason, I don't free Red until I've cleared the first 2 floors and am ready to go get Shorty.
To your 3rd point, I will generally stop by BigTown and get the quest but may not come back to it for many levels and to date haven't had a problem with Red and Shorty dieing.