If they are sticking way out, I'd agree with Dick - there's something not right. I have also come across coupler pockets that are a little too short - the standard Kadee centering spring will protrude very slighty. If this is the case with the whisker couplers, I would say it's more trouble than it is worth to modify the pocket, so you could live with it as is.
Bottom line - is the coupler working properly? No drooping, able to move freely side to side and centre itself?
Andrew