I have no idea how to get rid of the main problem but yet I can give you the solution to avoid the consequence of may windows To keep away from the trouble of Safari reopening all the windows once more, try removing the Safari Saved application state right after killing safari but previous to you start again it and do this
Quite Safari, as give details above
Just stare the com.apple.Safari.savedState Folder in the Saved Application State folder in your Library Folder and on there In Finder just go to Menu Go To > Folder or else press Command+Shift+G then put
Code:
~/Library/Saved Application State/com.apple.Safari.savedState
Remove all the files there data.data, windows.plist
That it’s just Start Safari
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