What is the resolution of your screen? Your screen shots show some sort of nesting of MainWindows almost as if you docked a widget from one MainWindow into a separate MainWindow?
You must have another instance of Sigil running on you Mac. This should never happen. When is the last time you did a full system restart? Did you tell macOS to reopen the last windows? If so, that is probably not a good idea when your system is having issues. Also you should delete any cached version of Sigil saved in your Caches and start completely fresh with a fresh ini.
Try using the activity monitor to make sure nothing Sigil related is being run at all at startup.
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