So this references a Budgie bug in Solus and Ubuntu dating back to '16 (!!) where keyboard shortcuts you apply via the Keyboard area of Settings open apps up beind running apps, pretty annoying…
I figured out that this problem seems to only apply to keyboard shortcut presets built into the Settings menu (gnome-control-center). So, for example, if you apply CTRL H to automatically bring up the home directory in nautilus via the preset option in Settings, it opens behind existing windows. If you scroll to the bottom of the Keyboard option in Devices in Settings and hit the “+” button to create your own new shortcut for Nautilus, however, and apply CTRL H, it opens in the foreground. Why? No idea.
So, I just ignore the built-in presets for browser, terminal, nautilus, settings, etc at the top of the Keyboard area of the Settings menu and have just created new entries with keybindings for them all. This finally works around one of the most maddening bugs in daily use in Budgie!