Well, the last time I did a re-deck with new carpet was before we had places like this one to post questions to. It was a '79 24' Crest. Not knowing there might be an issue, I used "outdoor" rated 3/4" ply purchased from a local lumber company. Used marine carpeting and re-assembled using all stainless fasteners because getting a lot of it apart was a pain with the OEM fasteners. In hindsight, the only thing that really wasn't right when I sold it 10 years later was that I should have used more glue or done something at the plywood seams. They were visible. I didn't look for issues where the deck met the alum, but there was nothing that ever drew my attention either?
Not endorsing the procedure, nor condemning. Just passing on an experience I had. YMMV.