DW & Kuyt, Korte's 3x3 routine has a preliminary phase where you do 5-8 sets of 5-6. See here for details:
The 3x3 Program
I would restrict your rest periods between sets during this preliminary phase, move down to around 2 minutes between sets. Remember the intent of this phase, it's a volume-building phase and as such you won't lose out on much of the training effect if you increase the density of the workouts. You can move back to a more relaxed pace when you reach the peaking phase.
Also I don't think you absolutely must
stick to an hour for training as a general rule, just take whatever time you need to get the job done. However I do believe you could restrict the rest periods in this phase, as outlined above.