If you are going to build a full RV with sub floor and lots of permanent cabinets etc..., sure get them out and have a normal build.
I was going to cut them after the front bench and make my bed storage like most people do. I knew I wanted to bolt it down rather than screw the floor to death, so after a few days of not thinking about the issue it just hit me, use the super heavy duty floor anchors you have if you can. The issue reminds me of the kind of thing my dad would suggest that "I would have no part of but later realized he was way ahead of me as usual"
I was able to come up with a plan that is working very well for us, the van has no squeaks "really" and everything is bolted to the floor rails and walls, so removal is an option. My build is more like a dorm room than a nice hotel just the basics, these are early pics and it's not quite as basic these days.