On our recent flight through Russia we had to deplane with all our stuff; we were even issued two boarding passes so that we could switch seats at one of our stops. I didn't mind the first stop too much - it was a super nice airport and I got wifi for a couple hours - but the second stop was in the middle of the night, at 3am, where they put us on a bus, took us to some basement waiting room for about 30 minutes (they literally wouldn't let us go to the rest of the airport), then took us back to the plane, where we sat for 45 minutes while other people getting on at that airport got on. Overall we had a 2 hour stop at that airport but they uselessly made us get off for 2 hours.

Also, I don't think it was a security thing - we took all our stuff, and didn't have to go through security in any of the airport; maybe they did search the plane, but I have a hard time imagining that an airline that does nothing about an entire row of completely drunk, noisy people is going to be particularly worried about doing things properly, like searching the plane.

Then I had an actual transfer onto a different plane with a different flight number.

So while I see your point about trains that make stops, if they make you get off with all your stuff, then get back on, it's not quite the same as a train where you can sit peacefully.