Is it safe to modify the custom url scheme from moodlemobile:// to anything else? and if so, should this be changed only in the config.xml file (I'm building the app via the Phonegap Build web service)
yes, it should be safe.
But note that if your site is using the Moodle Mobile Additional features plugin you will have to upgrade the plugin code and change this:
to match your new protocol
Ok, I will check that file out then
Thank you Juan