Really, that's not an issue with Electron, I think. You can perfectly well make use of a common platform toolkit and still make a completely counter-intuitive UI - and people did that, a lot. In the end, the important things are things like that the cancel button is on the left and the button to confirm is on the right (depending on your platform), not whether it's grey or blue.

And I'd even argue that, with the freedom Electron gives you, app developers have started to actually pay attention to their design, rather than just using the standard toolkit and considering it done - so Electron apps often have better UI. I'd take VSCode's UI over Geany's any time, for example.