It's not related to the icon theme but Nautilus' icon-view default-zoom-level schema setting. It is not possible to have different desktop icon sizes compared to the file manager icon view. It isn't something GNOME is going to fix either given they stripped out the desktop view from Nautilus, we just happen to be holding it back currently to retain desktop icon support in Budgie until I implement a separate solution.
It's not a bug. Just missing functionality in Nautilus.
