The order you describe may be better in some ways, but that isn't how the factory originally put it together, at least not on my trailer. Instead, from inner to outer, I had the C-channel bucked to the outer skin, and then the banana wrap pop riveted on, and then the rub-rail popped on over that. When I did my shell-off, I only drilled out the bucked rivets along the sides of the trailer. The curved C-channels, because they don't wrap under the subfloor, were left in place.
The advantage to your order would be that water would be less inclined to run down the body of the trailer and then into the upward facing seam created by the banana wrap. I put a healthy bead of vulkem on my banana wrap to try to keep some of the water out.
But, banana wraps are very soft aluminum and prone to damage, so if you buck them between the skin and the C-channel, you will never be able to replace them in the future, if need be. Plus, they are quite thick. I would imagine it would be pretty awkward getting them in place as you describe.
Good luck!
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