3. The explosive stuff (DJs, bounds, etc) programs your neural and musculature circuits differently. Your body gravitates from being comfortable in a squat motion to being comfortable and therefore more efficient in another (jumping, running, whatever)
With that said I have also noticed this weird conundrum with myself. I train a strength block and add say 20-30lbs to my squat and its now 300lbs (vert doesnt go up much or at all, we'll say it stays at 30" for comparison sake). I take up a explosive block and my vert shoots up a few inches, and squat strength goes down. Now, funny part, I go to another strength block...I can't do 300lbs so I go down to 275. Work my way up to 320 or whatever and my vert stays where it was after the explosion block and doesn't decrease while I cut back on reactive stuff. So it keeps going up faster than my weights are. This has happened twice now. Just my experience but still a thought worth considering.
Reason 3, exactly how I feel.
I've had similar experiences squatting. Except, the stepwise increase in vert hasn't been as smooth as predicted. It has happened a little though. It's amazing how much "strength" I "lost" if I stopped squatting for a week. If I didn't do any plyos, I wouldn't lose strength, I would gain strength. But if I decided to do bounding and sprinting, I would immediately lose strength. My legs started to feel comfortable expressing strength in more of a quarter or half squat position as they do in the amortization phase of sprints and bounding, but not in a deep squat position.
The thing is, jumping and sprinting will affect negatively the squat, which can negatively affect jumping and sprinting if you try to do both within the same block.
The stepwise process is thus probably best, because I haven't figured out how to gain strength and explosiveness in the same block yet but I thought I did once. But, i'm still working on it.