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> tkinter has added a #2
I think you yourself proved otherwise. Additional evidence is that ' #2' is not added on Windows. I have 3 windows titled 'myApp' stacked behind my installed python/IDLE icon. root.winfo_class() returns the class name capitalized, but the window title is not. root.winfo_class('newname') does not work. Note: I added more chars to the label to make it big enough to force the window to be big enough to display the title.
There might be a reason why tcl deduplicates class names on *nix. So even if you found a way to set a classname after the Tk call, tcl might still deduplicate it. Or we might decide not to force change the current behavior.
I suspect that this will be closed as a 3rd-party issue.