Personally I don't think there is a difference in the CPU's passing when the user is on manual.
I am with you on the subject of user crossing when set to manual. It's basically broken. Even with the minimum tap of the cross button, the ball flies miles away. It's such a shame, because otherwise manual passing works great. For this reason, I've had to go back to assist at 1.
I wish Konami could implement a system like FIFA where you can select the assist for each of the categories instead of a global one.