Wait a minute. That is a rather outrageous claim. I would love to see the proof. I thought Apple certification has to do with making sure the accessories meet certain minimum standard. If Monster Cable wants to make a gold braided Lightning cable, and their designs meet the minimum standard, to sell it at $1000 a piece, I am sure Apple has no issue with that.
They could do anything they wanted, but if they wanted to carry the MFi certification, it would have to meet Apple's guidelines.
I'm skeptical myself, but that is the explanation offered by one long time Mac peripheral maker/vendor. They deal extensively with the ODM market, and I've always known them to put thought into their products, and be straight shooters. If they wanted to procure and sell an Apple-clone cable, I'm sure they'd have little problem doing so, yet their cable, which is MFi, has a "fat" connector like everyone else.
Don't you find it strange that no reputable, well-known accessory maker offers a connector as small as Apple's? There must be some explanation for it, whether it's specifically rooted in MFi or not. The MFi program controls both development, and manufacturing licensees.
I don't think it's a stretch to say that Apple exerts great control over the accessory market, which has also lead to some other oddities like the requirement that Lightning docks that have support pieces sized like the 30-pin connector, rendering them incompatible with most cases.
(see Belkin's Charge+Sync dock, which is also sold in Apple's stores, so you
know they're going to play by the rules)
Most dock makers have worked around this by designing a simple non-electrical base that requires the fitting of an Apple cable.
There's only one common denominator in all of this.