@T0rin:
Hotkey toggle (and mouse click) takes a 1.2 second shift before skills can be cast after button pushed (timed using py script to detect pixel changes after keystroke on 3 separate machines).
Contagion won't autocast on something that has 0 dots.

I might have misread, but after testing, short of the pet casting aerial slash there is 0 difference in DPS (shockwave doesn't cast unless mob is in melee range like expected). There is a -10 potency drop from aerial slash and a .3 second delay from AS -> wind slash after cast.
Timing on contagion is perfect (with 1.6 seconds to spare) for dots to fully apply on first, and second rotation sets (probably the same for 3+) If pet isn't ordered to attack right before first do application there is a 5-6 second free period.
Conclusion: a minor loss in potency (AS -10 pot every 29.22 seconds) is not as detrimental as you make it sound.