Electron apps are also heavily customized, but ignore platform UI conventions. The buttons may have lovely drop shadows, but basic interactions (menus, undo, drag and drop...) are routinely broken or work in some discordant, unfamiliar way. This isn't meeting professional needs; it's that web tech sucks for building actual apps.
And even if web tech improved, there's still the cultural bias towards re-invention and churn. Web dev will always cons up a button from a div and an onClick handler, no matter what the framework provides. There's no mechanism to get web apps onto a shared UI platform because the gravity of the web is dispersive.
All those specialized tools can get away with having completely-unlike-anything else UI/UX because people are paying for them and they are considered best(and only)-of-breed.
Electron apps are cross platform only in terms of them looking alike on different platforms, because they use the same widget set. If slack was a truly, full native app on OSX, it wouldn't look like it does.
I don't understand your point - non-native widgets are not a deal breaker and there are plenty of examples, Electron being the most common non-native cross platform framework recently (it has technical limitations but even the subpar performance doesn't make it a deal-breaker). So it's possible to create cross-platform UI frameworks and most of the the most successful apps I can think of are using some version.
You are confusing cross platform UI with frameworks that have programmer art widgets and no cross platform polish - eg. GTK+, FLTK, and even to some extent QT widgets (and many more). When people say widgets don't look native they usually mean "the widgets suck", you can create beautiful cross platform apps - Electron has quite a few because it allows standard designer tools from web dev.
Flutter is another promising development, but the desktop port seems underwhelming - it's obvious the widgets were intended for mobile apps, they will probably need a custom widget set to cover desktop UI - but the approach is sound.