Would they fit side by side in the bed? If answer is yes I would not fuck with motorcycle carrier. I'd imagine securing hitch mounted one to prevent unwanted movement is PITA.
Also, if you keep one bike in the bed and another one on carrier, and you happen to want to use one in the bed you would have to remove one on carrier, etc. anyway. Too much work.
So, I would, if that is possible, load motorcycles on the bed.