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I just updated my Macbook to Mohave. As implied, I do not see this on installed 3.7.1 with 8.6.8. But this is a heads-up for future releases. Someone with both a Mac Python development environment + tip 8.6 would have to look at this now.
When the packaged tcl/tk in the repository is updated, idlelib/idle_test/htest.py should be run (in addition to test/test_idle.py) to see if the new tcl/tk introduces any visual artifacts. Htest passes 'htest=True' to ConfigDialog.__init__, but that only affects dialog placement. Kevin, can you run htest on your system?
I don't understand "the dialog's [wm transient] implementation is part of the issue; the parent windows for the dialog are not hidden when run against the Tk tip," The transient call is 'self.transient(parent)' and the parent is the editor-based window, which is not blank and which should not be hidden. If tk adds a new 3rd blank window, that seems like a tk bug to me.