Run tank dry - exactly the same as an out-of-pump tank. The inlet starts sucking in air and the pump starts cavitating.
Hot and noisy pump - no the pump is cooled by the liquid it is in. And if the pump is noisy its worn and needs replacement, same as normal pump
Fuel gets water in it - petrol floats on water, so like an old style tank it depends how much water. The pump will pump water same as petrol, but once it hits the engine things kinda stop.
Explosions specific to in-tank pumps? I have no answer.
Low profile tank - same as a high-profile tank with in internal pump. There's normally a low spot somewhere on the floor of the tank, and that's where the inlet would be. Low profile tanks will generally have a stepped design, so the bottom of the tank is not planar to the ground. Instead there will be anti-slosh barriers and forms, and the fuel will drain to the low point for pickup.
On a Boat - Probably. Depending on the size of the hull and the kind of motor, it could be just a funny-shaped car. Outboard motors, dinghys and zip boats wouldn't have something like this, but anything that is a motor vessel could. Larger marine engines tend to be diesel, because they want torque over high revs.