- You don't have to ship Wine with it, you can just make it a runtime/package dependency. Most distros have Wine in their repos anyways, so there's no need to bundle it. I don't see this conceptually being any different than shipping a Python app for instance.

- You can make Wine apps inherit the system theme, well, at least the colors. Although it will still look out of place, but it's not much different to the issues with running a Qt app in GNOME, or a GTK app in KDE. Wine in this case can be considered as just another UI toolkit that has the same problem that all UI toolkits have in Linux.

- Finally, the resource overhead of Wine is far, far lesser compared to Electron, which is a basically packing in a full-fledged browser.