I don't know about the order specifically, but using Cmd+shortcuts is more comfortable for me than Ctrl+shortcuts. That's not really due to the keyboard though; Windows could just as easily have used Alt for shortcuts instead of Ctrl.
I had a little bit of trouble getting use to using the key when I switched, but it now seems natural. I have trouble in Windows, where I never did before.
With that said, I do think that the placement of the key makes common shortcuts like cut, copy, and paste than the control key in Windows.