When I started Thunderbird today, it opened three windows. Each window was identical. I closed two of them and then quit Thunderbird.
As soon as I started Thunderbird, I had three windows again.
I found a Mozilla bug report from 2015 that had some tips for getting the additional windows closed.
Choose one of the open Thunderbird windows and select Close from the File menu. Do not use ALT-F4 or CTRL-W to close the window. Keep doing that until all of the windows are closed except for one. Then choose Quit from the hamburger menu drop down.
At that point, start Thunderbird again and you should have only one open window.
Note: You may find that one window does not respond to clicking Close - that’s your root Thunderbird window and it cannot be closed. Be sure to close all of the others.