Personally, I liked it back in the Win95 days when everything used the native toolkit and I could change its appearance significantly through a simple control panel [0]. Back then, if I wanted a "dark mode" I just adjusted colors to make things darker, but with modern GUI bullshit it's a newsworthy item when someone adds "dark mode" as a feature.
Customizability-wise I actually prefer Electron apps to native ones, with a few lines of CSS I can remove stuff I don't need and tweak the UI a bit, I'm not quite sure you can do the same as easily for native apps.
Also you mentioned dark mode, an Electron app could support dark mode too, taking as an example macOS native apps they also have to explicitly support dark mode, so I'm not sure what you lose in this regard by non going native.
I would argue that going full-native win95 style has more downsides than benefits, for most people simply being able to change the wallpaper is enough.
That's a fair point. GUIs have tended towards being less customizable, not more, and that's a huge failure in my eyes. However, the customizability of Electron applications is really a side effect of the fact that it runs on top of a web browser. I find it difficult to count that as a point in its favor.
Looking at it from that perspective, there are native GUI systems that load XML files for their GUI that could also be called customizable by your standard.
Native apps use system colors by default. Electron apps tend to use static colors.
I've no idea how good Xamarin is at doing the things that it does, but even if I hadn't invested X into my web-based components Xamarin would still force me to reimplement them again in case I need them in my website. That's not cross-platform enough for me, Electron in better in this regard.
- I'm a JS/TS developer, with it I can make CLI apps, websites, Electron apps and mobile apps. This means I can also use the same set of UI widgets I'm familiar with across all platforms, I can't do that with any other native UI toolkit so far, maybe the situation will change with the advent of WebAssembly, but so far JS has basically been the only language capable of providing this.
- I don't think I've ever used a Java GUI app that didn't look like crap and wasn't a game, I've also never made a GUI app in Java, so this is just a guess, but maybe it's just easier to make prettier apps with web technologies.