Here is what I have done to make Scrivener look more as intended:
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Grab yourself a Scrivener theme that looks nice. If you generally like the idea of default but wish it looked more like you’d see in a Windows screenshot, then check out the theme called White. The purpose of this theme is to recreate from scratch the “default” look, but as a theme. For Windows users it probably looks very much the same, but for Wine users it gets rid of all the 1995 era UI stuff.
The software also comes with a number of example themes. If you find one of those you like, they tend to work as well. It’s really only the “Default” light theme that lets a lot of Wine’s native UI through.
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Alternatively, if you don’t mind the UI, you can make some adjustments in winecfg like changing the colour of the UI elements. There may be an .mstheme that looks better than the default, but even just setting the background to white can make a big difference.
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Next, go into the Appearance: General Interface options area and set the Menu & Windows Font. Noto Sans, which comes with a number of Linux distributions, works well in my experience. There are a few other panes in here you might want to tweak. Binder, Outliner, Corkboard and Index Cards are usually what I change to Noto Sans or something along those lines.
That’s pretty much it! Most anything else you might find that looks odd is probably that way for everyone.