The comments in the prefs.js file:
# Mozilla User Preferences
/* Do not edit this file.
* If you make changes to this file while the application is running,
* the changes will be overwritten when the application exits.
* To make a manual change to preferences, you can visit the URL about:config
* For more information, see http://www.mozilla.org/unix/customizing.html#prefs
That said, you should be able to edit the file with the application closed, and the new settings would take effect when it is launched.
Depending on what setting(s) you want to modify, however: I don't believe the registry or command-line options will get you the same settings. Registry settings are more system-specific and not per-user; and command-line parameters will give you specific instance switches for the application, such as window size and which profiles to load, etc.
If you know the specific setting you want to change, you could search for it in the prefs.js file with a regex (using VBScript would be my choice) write a new file with the replacement setting, then rename/delete files so that the new prefs.js replaces the previous one.