I think it is important to realize that the bad guys seldom expect effective armed resistance, and often the reactions of the ones not being shot are not instant attack.
And I don't see any way to figure that into any calculations.
Actually, the calculations sort of highlight the point that it's rarely necessary to physically disable attackers--that they tend to run. The probabilities show that if it were actually necessary to shoot all attackers to the ground, the chances of success with a typical carry pistol are miserable. Given that we know that defenders succeed in multiple-attacker scenarios on a fairly regular basis, we can see that something else is happening a lot of the time and that something is attackers often choosing
to stop attacking when the shooting starts. That happens a good percentage of the time.
It's not really possible to tailor the calculations for every alternative, the point was not to produce a high-fidelity gunfight simulator, the idea was to provide insight into one particular aspect of a gunfight, namely how hard it is to put multiple hits on multiple opponents with a realistic hit-rate probability and a limited number of shots. Turns out it's a lot harder than I think most people assumed it is--it's harder than I expected it to be.
Does that mean that every gunfight will require putting multiple hits on multiple attackers? No, it doesn't. Clearly some gunfights, even ones with multiple attackers are resolved in favor of the defender without anyone being hit at all, some with one attacker being hit multiple times but the other being hit only once, some with only one attacker being hit multiple times, some with only one attacker being hit once. It can play out many different ways, and the calculation only looks at one type of scenario.
Of course, while it's not uncommon for attackers to give up when the shooting starts, it's not a given that it will happen in any gunfight. It's important to understand that while they're not the norm, there are determined attackers out there who won't automatically turn and run.