"Bean" is a weak man that takes the easiest path. He does a lot of posturing, and has a ruined arm because of NCR torture. He runs a still, which annoys Porter who he tells is just for Molotov cocktails, but he drinks a lot to numb the pain of his arm. Hardin has convinced him into leaving Denver because there's nothing left there.
Before their incarceration, J.J. Morehouse used to arrange for thugs, including Bean, to disable track, then blame it on raiders and tribals. That way he could demand more materials and demand that Dodge pay them more at the same time.
Not dealing with the traitor Salvagers before attempting to explore the Box will, in a cut scene, result in a violent conflict as the traitors turn up looking to take it for themselves. If Bombay Jack also wasn't dealt with it will include him detonating the bombs in his base in an attempt to take everyone else out with him. The Prisoner and any companions will be scattered around the rubble alive but severely injured.
If the Prisoner puts off exploring the Box for long enough, the traitor Salvagers will go ahead with their plan to strike it. The Prisoner will hear their interactions over a radio and may be able to get their before the showdown if he is quick. If not, he will reach the Box only to find that Jack was able to snipe or bomb all of them and will already be stripping their corpses, he will already have done this too if the Prisoner puts off investigation even longer.
Even if the Prisoner reaches the Box before the showdown, Murphy cannot be saved and will be killed by Jack in the scramble.
Design document notes on the quest Analyze Their Drug Stockpile mentions helping Bean to up the liquor content of his still, which has the knock on effect of being able to make better Molotov cocktails.