How do I reset to default window sizes in MacOS Safari's Responsive Design Mode?
.This setting is written to Safari's preferences, that are located in ~/Library/Preferences/com.apple.Safari.plist in dictionary by ResponsiveDesignCustomPresetConfigurations key. So if you need to reset all responsive mode settings - just close Safari and delete that dictionary from prefs .plist file with following terminal command:

defaults delete ~/Library/Preferences/com.apple.Safari.plist ResponsiveDesignCustomPresetConfigurations