I just reproduced this too with Airbook Mohave.  When IDLE's Shell is running, it is linked to an execution subprocess that is initially invisible, unless and until the user creates a visible window.  Tk() does this.  On Windows, a tk Window icon appears when I mouse over the IDLE taskbar icon.  On Mac, a new python rocket icon, also used for Python Launcher, appears.  And it becomes the active app for the Apple menu bar, making it more tied to the OS than on Windows.  In either case, I can switch between IDLE and tk windows by clicking icons or sub-icons.

When I click the red close button on the tk window, it disappears, but the rocket app icon is still there.  Clicking it maybe restores the window, which was hidden, not closed.  Or I may have to right click the rocket and then 'tk'.  Right-clicking the rocket and then 'quit' fails to close.  But trying to modify the tk window may fail with 'app destroyed' even though it can be made visible.  Closing the parent IDLE closes the Window.