Same in the desktop world - Qt emulates the widgets, but can theme them, then QML is another story. Also WPF (from what I've heard) uses (skia?) to paint own widgets. IMGUI is another example.

Then using the native wrappers, like wxWidgets is often cumbersome to create customized control, and if you do you end up with some platform specific version (not end of the world, but pretty much why not use the OS toolkit directly). Also any wrapper soon or later suffers from "leaky abstraction" - where you hide things behind interfaces, but can't hide different performance characteristics, and getting the current line in a log dialog might just kill you, because underneath it might be scanning all '\n', '\r' until your cursor position.