Got this from Epi-Support:

create a module.config

<?xml version="1.0" encoding="utf-8"?>
<module>

  <clientModule initializer="forceUseCustomMedia/Initializer">
    <moduleDependencies>
      <add dependency="CMS" type="RunAfter" />
    </moduleDependencies>
  </clientModule>

    <dojo>
        <paths>
            <add name="forceUseCustomMedia" path="scripts" />
        </paths>
    </dojo>
</module>

Create a module that concatenates the roots of the media and the content-provider contentrepositorydescriptors

define([
    "dojo",
    "dojo/_base/declare",

    "epi/_Module"
], function (
    dojo,
    declare,

    _Module
) {
    return declare([_Module], {
        initialize: function () {
			this.inherited(arguments);

			require([
				"epi/dependency"
			], function (
				dependency,
            ) {
       
					contentRepositoryDescriptors = dependency.resolve("epi.cms.contentRepositoryDescriptors");
					
                    var mediaRepositoryDescriptors = contentRepositoryDescriptors["media"];
                    var customMediaRepositoryDescriptors = contentRepositoryDescriptors["mycontentprovider"];
                    mediaRepositoryDescriptors.roots = mediaRepositoryDescriptors.roots.concat(customMediaRepositoryDescriptors.roots);

			});
        }
    });
});