I don't think there's a general fix for this due to how different apps code their multiple window implementations.
Practically, I've found that pushing myself to use apps where I find I'm missing a key command to switch amongst windows in full scree mode and use trackpad gestures to navigate helps greatly.
Basically - letting go of managing lots of windows and embracing the full screen has minimized my need to have multiple windows.
I also, generally have 4 fixed Desktops in Mission control and pin some apps to specific desktops - so that I know certain apps are always in certain virtual screens which reduces the time needed to navigate back to the "unruly" apps that tend to have many tabs or many windows across several desktops.
Specifically for terminal, I have identical Mission Control settings as you and color coordinate my desktop background colors and terminal colors so I know to go back to the green screen for the terminal window that was green/black. (and red on red and white on grey, etc...) Using colors helps my brain get to where I was working since the terminals match the virtual screens.