Actually, the way the EQUI.xml file is supposed to work in your custom UI folder is to gut it, then reference the EQUI.xml in the default directory. Then you can add entries for custom xml files to hold your custom elements. Copying the default EQUI.xml as is into your custom folder is not a good idea though.
This post from way back goes into detail on how it is supposed to work
How to make your UI never break