I believe many, if not most, 427 marked Cobras were actually 428 equipped. It was probably due to cost and engine availability issues with Ford. Carroll Shelby probably knew many of his buyers were not capable of safely handling a full out 427 car.
There's probably more replica Shelby Cobras out there today than Carroll Shelby ever rolled out of his shops. All seem to have 427 emblems but a small block engine under the hood.