I set up a few MIDI-Triggers to control Music with my KORG nanokontrol under the section "All Apps".
After that I put Logic Pro in the Applications list and changed the settings to "deactivate when running".
Now, when I open Logic, the icon in the menubar fades to greyed out, the common keyboard settings I made for my computer are disabled, but the Midi-Triggers are still active, so now I control Logic and Music at the same time with my midi-device. I think, Midi-Triggers aren't disabled.
I tested a little bit. If I manually deactivate BTT completely for all apps, Midi Triggers are still working, so it seems there's a general problem with deactivating Midi Triggers, not only in specific apps.
Thanks for your help
macOS Catalina 10.15.5
BBT 3.389 (1612)