It sounds like products are certified on a product-by-product basis, and this decision was more about not wanting consumers to wonder/worry about why one Mac laptop was certified and another wasn’t.
No, it's about trying to kill the standard. Many institutions can only buy epeat certified hardware. If the standard doesn't say what Apple wants it to say, then Apple will stop them from buying any of their products, even the ones that comply. Should be an interesting standoff.