The explicit need to allow popups is for homepages that are frankly poorly engineered to use popups as an interaction model. Popups in Webconverger are configured to forcefully open as new tabs.

Using the new improved prefs= API from https://github.com/Webconverger/webc/commit/a1b18d281e1b4858564b38fdda12b36352eed7bf we can use Firefox's powerful "autoconfig" commands to setup these permissions.

Lets walk through an example using http://popuptest.com/ as a source for popups.

We configure our Webconverger using prefs=http://prefs.webconverger.com/2015/autoconfigfile.js and this "autoconfig" file contains:

$ curl -s http://prefs.webconverger.com/2015/autoconfigfile.js
Components.utils.import("resource://gre/modules/Services.jsm");
Components.utils.import("resource://gre/modules/NetUtil.jsm");
Services.perms.add(NetUtil.newURI("http://popuptest.com"), "popup", Services.perms.ALLOW_ACTION);
Services.prompt.alert(null, "", "Popup test");

You should host http://prefs.webconverger.com/2015/autoconfigfile.js yourself, though Webconverger as a service to its customers can reliably host it for you.

As you can see in the Services.perms.add invocation, with prefs= we can now issue commands that add http://popuptest.com into a popup whitelist.

You can verify this works by visiting http://popuptest.com/popuptest4.html or by examining the whitelist using chrome=debug in Edit→Preferences→Content→Exceptions.

More on "Netscape Mission Control Desktop" aka Firefox's autoconfig

Webconverger's prefs= API uses autoconfig files.

Many thanks to Mike Kaply for taking the time to document this almost hidden Enterprise feature of the Firefox browser.