The crux of it is that macOS became more strict about what you were doing in GUI- vs non-GUI-threads, and now asserts if you fetch GUI events (I think?) in not the main thread, because of the risk of memory corruption. Ostensibly.
This bug only manifests if you compile Emacs on 10.12 (so if you install the "emacs-app" in MacPorts, for example), because then it'll link against the asserting framework. If you use Emacs from another source that compiles it on 10.11 (such as from https://emacsformacosx.com/), then it links against an older framework that doesn't have the assert, and it'll work "fine".
Considering the fractal accumulation of "clever hacks" that make Emacs work on modern GUI systems, I'm curious to see how this issue will be resolved, because I doubt it's something so simple where Emacs has proper separation of GUI vs non-GUI threads, as QED by the article ;)