Even if the pads are permanently stained from pigment transfer, it shouldn't cause any problems. I can't remember ever using a red-stained pad on a white car or somesuch, but I bet I did it back in the day 'cause I'd remember any problems.
And yeah, GoudyL's right on the money about #7 being a nice penultimate product for single stage. If you really want to apply this glaze step via rotary (I wouldn't, but that 's just me), I'd use their #3 instead as it's formulated for that. Actually, I find #3 more user-friendly than #7 anyhow (even by hand) but #5 is the easiest of all. #7 looks the best though.
See if you can find Mike Phillips's write-up about how to use #7 if you're not familiar with it. It does have a bit of a learning curve.