I think you may be confusing certified like new with refurbished.
The cln program is fairly new (like a year or 2) so people may not be used to it. When you'd get a replacement phone earlier you'd get a refurb. It came in a brown box with a sticker with bar codes showing that it was a refurb. The only thing that came inside was the phone, no battery door, battery, manuals or anything else.
But these cln replacement phones come with the battery door as well. You can also get cln retail phones as an upgrade device (my brother got an original Incredible just before they went out of stock) which are usually half the price of a new model. My brother's came with everything that a new model comes with, the only hitch is that they have been opened/activated/used prior to receiving them.
When Verizon switched me from my Tbolt (after almost 2 months) they said they could only do a cln Inc2, which was fine with me. The rep told me that they didn't come with anything (battery, battery door, sd card or sim card) so he would order me a battery & door. When it arrived it already had a battery door so basically I got an extra battery door. It also had a sim card in it as well. So even some Verizon reps don't know what they come with.