I have a croc-embossed Madison Lindsey, and one of the tags is in the croc-embossed leather. It still has the logo on it.
Well, that shoots down my theory.

Perhaps Coach was trying to distance itself from--itself?

The real reason is probably something goofy, like they just plain old forgot to emboss some of them and once they got out, it was an "oh, yeah... we MEANT to do that" situation.