Confirm first that you can use those links from within your app, not within the inAppBrowser view. I believe the inAppBrowser view is a restricted view, for app and device security, since it is meant to render HTML5 from anywhere on the planet. In which case it will not work. Also, make sure that your whitelist is configured to allow those intents, that may be the problem.
Intel XDK 2893
Cordova cli 5.1.1.
The external website use Framework7.
The problem only happens when I use links (tel :, mailto :) on the external site.
The links opens the respective functions. But underneath always appears the error webpage like this - http://mariusbancila.ro/blog/wp-content/uploads/2015/09/ERR_UNKNOWN_URL_SCHEME.png
If you use these links within the app does not appear the error page.
(Sorry my English.)
Nuno, if you use _self as the target AND include the location you are opening in the white list, it will probably work. See the doc page here > https://github.com/apache/cordova-plugin-inappbrowser#cordovainappbrowseropen
Another option is to use _system as the target (see the doc link above).