I can't reproduce this. Is this really happening on the internal Macbook trackpad for you?
Does BTT have Accessibility API permissions in System Settings => Privacy & Security => Accessibility?
For external non-Apple keyboards I'd understand that this could happen, but for Apple keyboards it would be quite weird :-/
If you can't get it to work, I'd recommend to remap Caps Lock to option or cmd and then follow @Frank1's general suggestion on how to setup shortcuts that only work with that remapped key pressed by using BTTs "Differentiate Left / Right Modifier Keys"