I love writing software for Linux, but tbh I'm glad I never got into writing GUI apps. Between Qt, GTK, X.org, Wayland, Mir, whacky hidpi support, etc, it sounds like an absolute nightmare.
You don't really have to choose between things like Qt and X.org, Wayland, hidpi, etc. Using a library such as Qt means you only have to care about your application, and leave the rest for the toolkit developers, who will code the actual backends for X.org, Wayland, Mir... whatever. Of course nothing is perfect and issues may arise but I don't think it's as bad as you depicted it.
Qt has never worked correctly with HiDPI and Qt5 is a nightmare to integrate a player window (need to implement yourself on every platform).
No magic.
VLC does care about because the movie is rendered by the compositor not by QT for performance reasons. It is explained in the presentation.
Long time ago I wrote some cross platform Qt4 apps , the apps worked (I used things like calling APIs, uploads/downloads, screenshots,embedding webkit, system tray support) no nightmare, no hunting for random libraries. Maybe some entitled users would complain that it does not look native enough on their system but the app was not forced on them and at least GNOME based distro could have put a bit more effort into making Qt look more native.
I would say that Qt makes GUI on Linux about as easy as Delphi was on Windows in its day. It's somewhat of a bubble - if you use Qt, the incentive is to do everything in "the Qt way". But it also nicely abstracts you away from all those underlying differences.