It's those extra 3.5"!
Interesting idea on the side hatch (our hot water tank is on the starboard side - so not an issue) I wonder if the boat is noisier as a result - or was insulation used on the hatch? (My problem would be getting to the hatch - I store everything in the quarterberth!)
As to loosing things in the bilge - tricky indeed. It was great when I changed out the gearbox this past weekend - I recovered all sorts of bits and bobs that must have been there for years!
There is a good spot for the tools when under the cockpit - I put them on the shelf in my main cockpit locker - I can't quite see them from the engine, but they are convenient to access and feel out by hand. I basically bring the entire toolkit and lay it there - because getting in and out of the engine room is such a pain.
(My lights in the engine room are DC...)