I have a few apps that ignore keyboard shortcuts. It's not terribly inconvenient, but it is annoying. My question is, "How?" How can an app not...submit to?...the OS's requests to hid (command H) or minimize (command M)?
I tried setting up shortcuts for the app in the above panel, but there's no response when I set them up.Apple must provide an API that allows it. So the developer is not really subverting the OS, but just making a bad decision.
Maybe you can yourself "override their override" using this area in System Preferences:
View attachment 822896
That shows some custom keyboard shortcuts I set up for Notes and Safari. If Safari was the problem app you are describing, I would add one for "Hide Safari" + Cmd+H