Yes, I cut it away so that it curves right around the carpet trim, then, I sanded the back with my belt sander so that it angles up the topcap nice and tight. Should I sell the boat, and the new owner don't want them, he can just remove it. Something about cutting that large of hole bothers me too.
And yes, 2 is the way to go. I also have 12 rods (casting and spinning) in my starboard locker, so if I trolling for Walleye or Salmon, I'll just strap all my trolling rods to the bow. Those are 8 and 9 1/2 footers (telescopic) and the fit nicely there. Same with my Musky Rods.