I think the earlier recommendation for using duct tape was to prevent accidental damage to the hull during sanding (not going back to check right now), rather than something to do when applying your wood treatment.
If I were you, I’d remove the gunwales and do a thorough job, especially if you are going to use something like varnish or urethane. If you are going to seal the wood that way, it makes no sense to not seal the surface that’s wet more of the time than any other! A common recommendation is to skip thorough sealing with varnish or similar products if the gunwales see much abuse. It’s much easier to touch-up rough spots if you go with oil. The natural delay that there will be in fixing damaged spots if you used varnish or urethane will simply let the water soak in at those spots and have minimal ability to get back out again.
If you take off the gunwales, you can even use a powerful sander without fear. I did this on one canoe that had unusually delicate gunwales, yet with judicious use of a belt sander (I can already hear people gasping at this), I finished each strip in just a few minutes, without there being even a hint of “overdoing it”. An orbital sander would have required a good two hours of work on each strip (I know because that’s how I started out the job).
If all you do is apply oil, perhaps you can get by with not removing the gunwales, but every once in a while, loosen up the screws to let applied oil work its way around to hidden surfaces.
Finally, I bet you have thought of this, but with some lumber and a bit of rope, you can make a tarp shelter that is not in contact with the boat and also won’t allow rain to blow inside. I have a utility trailer with a wooden cargo box for which I rigged an overhanging “lid” with a tarp over it, and even in the wettest weather, the wood of that trailer stays as dry as if it were parked in its own little shed. Most people who protect boats with tarps don’t put much as much effort into the job as they could, and it ends up being a moist environment, but there’s no reason a tarp shelter can’t be as dry inside as any other kind.