Sounds like you are talking about routing out a channel in the floor. Since that is a new camper, my approach would be to contact scout about feasibility and make sure it didn't affect the warranty. They could also tell you how thick the floor is. Maybe the flanged type would work better.
Other options would be angled L-track on the surface or mount the L-track to a wide flat plate with a rubber bottom that you can take in and out when you need it. When you're in camp mode you could set it outside with your bike.
