Hmm, sometimes when I've seen the inbound late, I don't bother going out to the airport at the prearranged time. There's no point. I'm sure I've called up and said "can I go out later?" and the answer has always been yes. I've never had any issues. You can still check-in online.
Not sure why the mix up with seats etc. Also sounds dodgy that guy managed to show a boarding pass to get on the plane but had lost it? while sitting in the seat?
If I'm switching flights I have unchecked in from the original flight and gone for the later flight but I believe that was Qantas or putting Emirates into credit (thanks Auckland traffic!) and then just booking Air NZ because I still had to go regardless so just caught the next flight out.
I'm not aware of being checked in and then switching to another flight.
I think you also can't change your seat after you've checked in which frustrates me on domestic as I can do that with Qantas. Can't remember if I've done it on the Tasman but I love that I can still switch seats even after check-in with Qantas. Except I have to be careful as some of them are just blocked rather than actually taken. Been caught out with that one once but it was an awesome flight anyway.