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It sounds like it may have been fuel vapors in an enclosed space that ignited. The recommended procedure for gas-powered boats with an enclosed space (like an inboard engine) is running a ventilation blower for 3-5 minutes before starting. Based on what I read, it sounds like he flooded the motor trying to get it to start, and when the gas vapors built up enough, it ignited.
Edit: it appears this boat had dual outboards, but if it had enclosed fuel tanks and electrical in the same space, the same still applies but there may not have been a blower to run.
Dive ops in Cozumel each have a unique color band or neck symbols on their tanks to ID the operator. This allows the fill operations to segregate the individual OP's tanks and helps the boat Captain's to identify divers on surface and keep groups together under water. The addition of a green band to the OP's color band usually indicates Nitrox.The shoulders of all the tanks are painted yellow. In the USA that indicates chlorine gas. Not sure if it has any meaning in Mexico.
I understand it was a Scuba Du boat and gas fumes under the floor boards.