Hey @rbrian,
The simple answer is you can't.
Keyboard Maestro is only able to isolate windowed-applications. (E.g. those applications that have a menu bar and a window or windows.)
Apple changed some things a few macOS versions back that made floating windows for background-only apps easier, but they also broke the ability for such apps to have context while their window(s) were in focus.
There are ways to work with these kinds of apps, but it's awkward.
You may want to look at this thread:
Working with the Pomodoro Menulet Application
-Chris