Not much of the story adds up. If the mission was a torpedo firing exercise the boat would be working shallow and in comms with surface support vessels - remember one of them reported seeing lights on the boat as it submerged so they were very close by - but no comms came from the boat at any time after submerging. At least no comms were mentioned by the navy.
If those amazing subsea waves were strong enough to snatch a boat near the surface you would think something would have been visible on the surface. If the boat experienced a rapid loss of control they would have blown everything except the messcook. It would take a near 180 degree roll to prevent a normal or emergency blow from stopping the descent, consider how far the boat would have to roll to allow air to escape. The only thing that would stop a blow is failure of the blow valves, failure of the vents to shut, or flooding of the control room that was so fast no one could act to blow or to communicate.
No mention has been made about that “subsurface floating object” since the first reports. If it existed it was probably the emergency buoy and was most likely released when the hull broke up. Who knows, nothing has been said since.
It appears that the hydrazine emergency blow system retrofitted to that class of boats by other navies was not purchased by Indonesia. Maybe that is not something they want to talk about because it would be a major embarrassment to some admiral and really get the families upset . Not much about this disaster makes a lot of sense.