Good question, I believe the Mac installer leaves config.xml intact.
But it might be a good idea to save /Applications/gdc/bin/gdc.app/Contents/etc/config.xml to another place before trying that out:-)
Putting the file back after install should work.
Alternatively you can edit the shortcut of interest ,enable "Store shortcut in settings" on the 1st wizard page and save it.
Then GDC puts the information in "~/Library/Preferences/com.four-js.Genero Desktop Client.plist" and it survives the install too.
HTH and Kind Regards, Leo