If you look inside the bundle-frameworks\oxygen-frameworks folder distributed with the Author Component sample project, it contains a document type framework folder. Customizations which affect the framework/document type configuration for the component should first be done in an Oxygen standalone installation.
An Oxygen standalone installation comes with a frameworks folder which contains the dita framework located in [OXYGEN_DIR]\frameworks\dita. The dita framework contains a bundled DITA-OT distribution which contains the DTDs used for DITA editing. If your DTD specialization is a DITA OT plugin, it should be installed in the [OXYGEN_DIR]\frameworks\dita\DITA-OT\plugins folder.
To make changes to the DITA document type configuration, open the Preferences dialog box and go to Document Type Association. These changes will affect the [OXYGEN_DIR]\frameworks\dita\dita.framework configuration file.
After you do this you can re-pack the Author Component following the instructions from the README.html file located in the oxygen-sample-applet project. The Author Component Sample Project and the Oxygen standalone installation should be of the same version.