My new Allegiance is set-up with the nock/cushion. Why?? because the pro shop said I was at the perfect draw length and looked very comfortable when anchored. I was always a loop man. I see no change, either way is good. I do like hooking up to the string though, it is much easier.
The only problem I ever had with the loop was it stretched, and without me noticing the gentle lengthening process. I ended up getting way out of position, and compensating.

Whichever way you decide, will be fine.