I did this workout today. Congratulations, looks like you had a great session 
I’m not sure I’d tell you to do anything differently. In fact, I think we both approach the bursts in a similar fashion. I do use ERG for all of my workouts and I, like you, drop my cadence down before each burst. I find that this gives me more muscle activation.
In a hard group ride or race, you can find yourself in the ‘wrong’ gear yet you still have to get the power down and get on top of the gear.
I would say that I don’t suffer from any knee pain and I track my knees during every workout. What works for me might not be the best or advisable for another rider.