I say leave it. I have a 72" frame on my 16ft Aire. It fits similar to your description. I purposely chose to run wide to make more space for strapping down gear on my sideboards if needed. It also doesn't feel cramped when i'm walking/fishing on the sideboards. I have a 5 bay so the crossbars support it fine at a lot of contact points. I chose the DRE oar towers so I can cut down and adjust the geometry of towers accordingly. Keep it and see how you like it; especially if you plan on getting a the NRS-E. If you don't like it, cut them; but it is tricky to redrill holes if you don't have the right equipment. If you do cut them, look at the minimum for the NRS-E.
I see no purpose in running the frame tube centrally on top of the raft tube. I made my frames wide like that on purpose. I made running boards on top of my tubes for gear and it makes it easier to walk on the tubes. My frame is powder coated steel (for now) with aluminum diamond plate decks.