I have yet to carry my inflatable on top of the boat. Just my personal preference. I do have tie down straps, just in case. I don't like not being able to use the handrails, I am not excited about the windage, and I don't want to have to rig another running light. I deflate and carry in the C-Dory. At night if it is not inflated, I put the bag on the forward deck, in the motorwell, or on top of the cabin. If I am at a dock, then it goes outside of the boat. I have used both the LT-2 and the West Marine Mini dinghy. Granted, both are small but inflate/deflate quickly.
If I start taking my dog with me, then it's a whole different deal. The dinghy will be on the roof. :dog Robbi