A few things need to be kept in mind when considering the hypothetical magma submarine.
Firstly, not all parts of the submarine will fall at the same time. Floors, walls, and other constructions fall instantly - they aren't in mid-air for any amount of time, but instead go from where they were at the moment they lost support to the ground instantly. As they fall, they destroy any items or creatures in the way, and displace water or magma upwards. Next, all creatures and items fall at a fixed rate of 1 Z-level every 6 ticks. Finally, water and magma falls at a slower, pseudo-random rate.
Secondly, Dwarf Fortress has no notion of tiles that are connected to each other but not supported by the surrounding terrain. Constructions are either supported by the surrounding terrain, or not connected. A mass of walls and floors released from surrounding terrain don't fall as a single block. They fall as individual walls and tiles, with each one's fall being calculated independent of the rest of the falling mass.
So, let's say you have a hypothetical magma submarine containing floors, walls, water, and dwarves. You build it above the magma sea, and then release it. First thing that happens is that the game will one by one move each floor or wall tile downward until it hits the semi-molten rock. Dwarves in the way will be annihilated. Water in the way will be pushed upwards, displaced by the falling walls. As each tile hits the semi-molten rock, it will be destroyed.
Secondly, any dwarves which somehow survived the cave-in will start falling. This can only happen if the submarine had an open top, since any roof on the submarine will destroy any creatures in the way. The water will also start falling, but it will fall at about half the rate of the falling dwarves, so they'll hit the SMR first even if they started out above the water. Of course, they'll be killed by the fall and the magma.
Finally, the water will land on the magma, and form obsidian. Obsidian tiles which form adjacent to solid, supported land will stick in place, unless they're directly above the SMR, in which case they'll be destroyed. Obsidian tiles which aren't supported will fall into the SMR and be destroyed. Because the water will fall with a pseudo-random pattern, the resulting solid obsidian sheet, if any, will be irregular and unpredictable in shape and extent.