If I am understanding your question correctly...
I am not going to use the cooler, so that whole area will be covered by the floor and out of sight. My cooler is brittle already, and I am fortunate that I do not have to trailer my boat everyday to use it. I will drop it in the water and leave it at my cottage for the summer (Barring any issues). When we go out to ski, tube, wakeboard or whatever, we can just pack a small cooler with drinks if we feel like it. We'll be within eyesight of the cottage most of the time, so we can always run back in for food and drinks. I spend 90% of my time riding my stand up jet skis anyway, so the boat will be a nice morning activity before the lake gets rough.
Essentially I am replicating what was there before, but I am just not cutting out a recess in the center stringer for the cooler. The cushion that acts as the cover to the cooler will still be there, so I can also now use the area under the bowrider as a storage locker.