rjuarezp now Nautilus is not showing in dark modus
I noticed that there was no such problem with Caja when I updted my MATE VM, so I tried installing it in Budgie, and it's good there also. Dolphin is also unaffected by this issue, but adding Dolphin to Budgie would probably add a lot of dependencies. Adding Caja adds just two packages. So, if you're really annoyed looking that that white Nautilus window, you might want to give Caja a try for now.