Hmm...I think in this instance we've created a new object by combining cookies with cake, a cakie if you will

>I can't agree that cookie dough is a cookie though,

Definitely, it doesn't count as a cookie until it's baked, part of being a cookie requires baking, but once the dough is mixed I don't think it can become anything other than a cookie

>So if we take uncooked cookie dough and layer it I couldn't call it a cookie in the form of a cake; it's fundamental to cook the dough before it's a cookie

Completely agree there, I'd call it cookie dough in the form of a cake, however once baked I wouldn't call it a cake, because it doesn't have the composition required of a cake

I would say that it's the constituent parts and differences in consistency that makes something what it is, not its final physical appearance

If you put icing and sweets on top of a cookie it doesn't stop being a cookie, it's just an iced cookie. If you layer a bunch of cookies I think you could probably call it a cookie cake, but it's not just "cake" as it doesn't have the right composition, it's simply cookies in the form of a cake