I'm not sure what the issue is here as e-mail settings (among others) are not stored in NSQ files but rather in the NPrinting.ini file (%ProgramData%\NPrinting\NPrinting.ini). You can change the settings under Options without opening an NSQ. You can also directly change the settings in the ini file. Each of your environments need to be set up just once and there should be no need to change NSQ files or environment variables. Let me know if I'm missing something.
HTH - Daniel.