The essence of the program lies in its final stage. Before running a multi-stage program you have to check each stage objectives, compare it with your goals, take into account your current situation and the previous programming with its results… Say you want to run Khan and you’ve run DR before so you may skip Stage 1 since you did a great cleaning with DR, you may skip Stage 2 since you’ve been using alpha programming for a long time and you don’t need alpha programming so much, you may skip Stage 3 too if taking action is your second nature. So you go for the final stage.
I don’t claim it wouldn’t be beneficial to run every stage but I think it would be more beneficial to skip the programming you don’t really need for the sake of running the final stage.