First I had assumed that scrlayer-notecolumn is indeed "forking" the output routine to simulate multiple independent "page environments" for different layers, as I had imagined for something I'm still trying to put together.
But they are "only" using \vsplit to split the note column, which is quite sufficient in itself; I was just suprised it works with a plain vanilla longtable without somehow tweaking the output routine... Apparently @DavidCarlisle knew what he was doing ;-)
Next they'll be telling me longtable even works in mdframed ;-)
Though for me it's a bit like TikZ: The interface is so sophisticated I'll probably never get around learning to use it. On top of that, doing something with \vsplit is so much fun I wouldn't let an opportunity to use it slip :-)