I can see why the Electron-haters are downvoting you, but you're completely right. Don't build your apps in GTK if you don't want to have overridden GTK configurations affect your UI. I would really like Electron to add an on-by-default standard interface to override CSS rules for Electron apps, though.
(I don't have a horse in the Electron-is-great-or-crap race)
> I would really Electron to add an on-by-default standard interface to override CSS rules for Electron apps
That's a hard problem to solve, since there are many ways of styling Electron - Bootstrap/Bulma/Material Design/custom stuff. So it's hard to just override CSS rules.
On the other hand, it's the kind of problem perfectly suited for Machine Learning - just take the whole screenshot/image of the app and use a stylistic ML to change it - make it Dark Theme/whatever...
I suspect in 10 years OSes will support ML-based automatic themeing/customization of all apps, regardless of what they are written in.
If we remove options just because few people use them, we might as well shut down the Gnome project along with everything else related to the Linux desktop.
I mean, you either want artistic control, or you want a consistent theme across apps. They want artistic control, thus would be better served by Electron.