I don't follow. Why would Manufactured Spend specifically cost the Mint money? It's not great for the credit card company, sure, but why the Mint? If the Mint was previously eating the interchange fees & shipping, ok, but that's not a manufactured spend specific issue.
I agree it's not specific to MS. But MS was probably inducing much more demand and thereby making them eat more fees than they planned to. (I don't have any inside information though.) Adding a premium would make it a little less attractive to MSers.