The left pulley never lined up on mines too, off ½ a tooth. It has kept me up at nights for years.
I have a question on your second problem (quote below). What do you mean by "the Gates pulleys don't rotate along with the belts?" I assume the Gate pulleys spins when off the bike or without the belts on them when manually spun (?).
Also, I do notice the new Gates pulleys, although they move freely and smoothly, they don't spin when I turn them.
Definitely totally unlike the OEMs I pulled off. And yes, they do clear the backing plates when turned.