When in a call in Skype there is a global keyboard shortcut of CMD + Option + CTRL + Up Arrow to enable push to talk mode. There is no way to customize of disable it. I tried adding a global shortcut in keyboard maestro, it was triggered but the push to talk mode was also triggered in Skype. Is there a way to make keyboard maestro take control over these types of global shortcuts?
Basically, no.
See the FAQ.
Specifically "If two (or more) applications define the same Hot Key, both applications actions will happen”
So if Skype uses Command-Option-Control-Up Arrow as a hot key, Keyboard Maestro cannot interfere with it.
A lower level tool like Karabiner might be able to do this.