To share my experience, I have sent in a D2H for general checks and thereafter I was told that the shutter needs to be replaced (SC under 20k). I knew the shutter is dying beforehand. Another incident, I had send my another camera D700 for some defects and 2 main boards needs to be replaced. Until now, it's working fine.
To share further, it's also about the choice of words used by the technician/customer service. Sorry but generally, they are not scholars and may not be good in their choice of words. A misinterpreted word used can cause plenty of misunderstanding.
Competent or not, in my opinion, it all voice down to what u impression u have told the front desk and the mindset will be fixed immediately. I would think it's some kind of software that Nikon develop to perform health checks on the camera. What probably the software does is to tell if there is a malfunction / intermittent (hopefully) / software not able to detect any other issues (like corrosion). Perhaps only opening up the camera then u may see algae / rust spots etc. but in terms of connectivity, there may not be any open circuit yet.
To be fair, they are not the user of the camera and the only exposure time they had with the camera is only that few minutes.
Maybe can try putting yourself in their shoes, what will be the reply even though u knew the submerged cam is working now?
Btw, I was advised not to repair my D700 then because there is one particular main PCB that is very costly to replace, luckily it's not that particular PCB that is damaged, but still, the bill is close to $1k (2 boards replaced) and a long downtime too. The consolidation was thereafter, I got 6 months warranty (come to think of it, i think it's only the 2 boards warranty and not the whole camera).