I had the exact same problem you are describing. Unfortunately, I never found a good answer on "how to do it right". In the end, third party apps mostly fixed

I had the exact same problem you are describing. Unfortunately, I never found a good answer on "how to do it right". In the end, third party apps mostly fixed the problem for me. Hyperswitch (https://bahoom.com/hyperswitch https://bahoom.com/hyperswitch) for switching between windows instead of apps and uBar (https://brawersoftware.com/products/ubar https://brawersoftware.com/products/ubar) for minimizing and maximizing apps by clicking their icon in the task bar. I hope this helps.