⌘F, ⌘H and ⌘M seem to be MacOS specific commands for Toggle Window Mode, Hide Window and Minimize Window. I have deactivated theses shortcut's with BTT by assigning no action to them, but I would like to resuse them for meaningful functions within the application. Sadly I did not find them in the normal Keyboard definitions (MacOS -> settings -> keyboard).
Is there a possibility to avoid that MacOS grab's the functions for it's own use ?
Just assign the shortcut the action you want. It seems to have a higher priority than macOS, meaning it replaces the function. Tested successfully with ⌘H
I have tried to do this, but in my case it doesn't work.
It should work, shortcuts defined in BTT always have higher priority than system shortcuts. Also shortcuts defined for specific apps in BTT have higher priority than shortcuts defined globally in BTT.
About the layers: I do not understand whats first.
e.g.
So I do not really understand the layer concept. I also have found some descriptions about the MacOS
NSUserKeyEquivalents, but ist this before BTT or after ?
If you set cmd+M to "nothing", assigning it to a Touch Bar button also will do nothing. (Same if you assign cmd+M to cmd+M, this would just cause an endless loop of BTT triggering itself :-))
If you want to trigger a main menu action after overriding it's shortcut you could use the predefined action "Trigger Menubar Menu Item" and enter e.g. "Window;Minimize"
and what about NSUserKeyEquivalents ?
It's just to know !
NSUserKeyEquivalents are what can be defined in System Preferences => Keyboard => Shortcuts => App Shortcuts. Here is an example of assigning cmd+h to some other menu item in Google Chrome:
Thank you for the moment, I need some more time for investigation now 
