Sounds like a lot of complication and added weight you don't need.
Having had a few different trailers and used a bunch of other peoples trailers... I would just keep it as simple as possible if I were to build a trailer. Basically, just a nice simple flatbed trailer that only has enough clearance underneath to match the vehicle pulling it. I'd also want it to be low enough to be able to load and rig without needing to stand on anything. Oh, and as lightweight as possible...which would mean an aluminum one (even though my bank account would scream at me for it...buy once cry once I guess).
Storing stuff underneath is great...but it necessitates the raft being way up off the ground. I can pretty easily fit my dryboxes and cooler, along with a few packed dry bags and such, in the back of the truck... and most everything else can be pre-rigged onto the raft including oars and frame and a few cargo items.
Having something low slung, in addition to making it easy to load stuff, it below the level of the roof of most vehicles...so you don't have a raft poking up into the wind getting dirtier and killing your gas mileage (as much).
I was thinking something like this (in Aluminum)...
Simple, low, and streamlined and basically as low as you can get it without going crazy. I totally get that you'd want it narrow and sleek. Adding a more complicated deck system is just gonna add weight and having to set it up and break it down every time sounds like a pain. Better to just make it 4-6" wider then the raft IMHO.