I have "Shift+CMD+Left Arrow" and "Shift+CMD+Right Arrow" configured under "For All App" to move my active window to the left/right monitor (using the "Move/Resize" action), which is working great for all apps except for iTerm2. I do not have any "Advanced Conditions" for these shortcuts, however if I configure the very same shortcuts under the iTerm2 app they are working just fine.
If I disable the ones under iTerm2, when pressing them they are not appearing in the "Recently Used" and capital D and capital C are appearing on to iterm's command line.
This is not exclusive to these shortcuts, it's just an example.
disabled shortcuts for an app mean: “ignore global shortcut, perform app default action for this shortcut”
(this is a relict from the very early days of BTT, but is used in so many configurations that I can not change it to something that would make more sense without breaking a lot)
Maybe I forgot to move this to the "new" documentation, I'll have a look! A section about app specific triggers would probably be good anyways because there are many special cases there