Chris, fly fisherman here too. I have a Skadden frameless that lives where the back seat was in my F-250 crew cab. I removed most of the back seat except for the passenger side jump seat. I also have a Steelheader Sookum that has very large tubes and a frame. (Same as Idahorons third pic) I also have an aluminum center console jet boat that I trailer. That is where the Skookum resides when on the move. The Skookum is to heavy and too big to use without the trailer. It certainly would not work on top of the camper. Because I just don't like the limited access of pulling a trailer, I am all but ready to put a for sale sign on the jet and the Skookum.
Okay, so all of that to say that I feel your pain. THIS IS NOT A SOLUTION and I am hesitant to tell you that a couple of times DURING EXTENDED STAYS, I jacked the camper free and just used my truck bed to haul the Skookum. Before others here feel the need to chime in and tell you it can't be done. I'll Agee that it is not a good solution and certainly only if camping in the same spot for weeks to a month. Then it is worth the hassle to me to get into some tight overgrown river access spots. HOWEVER, agreed THIS IS NOT A GOOD ONGOING SOLUTION. So all feeling the need to say it can't be done, no need because I admit you are right, right, right and I am wrong wrong wrong. But Chris, wink, wink, it can and I do.
That said, we are left with the same problem with the same boat and maybe two heads are better than one? I have been thinking about configuring a couple of slider bars that would extend aft and cantilever past the back of the camper on the same line as the roof rack channels. Then basically do the same thing that you have done in the past only hang the boat from those two bars. This way ground clearance is not a problem and once hung easy to secure to the back of the camper for a short jaunt up river or back to camp. For long hauls it would still deflate and live in the back seat. However this is my primary concern. Even though the boat weighs next to nothing there would still be some up moment at the front connection that I am concerned about and may kill the concept. Give it some thought?