Seeing as I'm not known for my sterling conversational skills, I don't think I'd be the least bit out of character in saying "Well, duh."
Would we rule the planet if skulls were a vegetarian structure? Hell, we don't rule the planet now. The best we could ever lay claim to is a poorly used loan. A question of whether or not to believe in skulls? Preposterous. You believe in asses, don't you? Presumably not just because they're easier to point out? Without skulls, there would be a lot of unemployed masks (not to mention biologists), Hamlet never would have recognized Yorick, MRI's would be dead boring, and we would never have that sparkly sensation when someone drops something and you both go for it the same time and 'klonque'---therefore, I believe.
Function and structure is easy enough to understand in the concrete, the framework adapts to the needs of the whole, with variations and anomalies that swirl everywhere from the malformed skull of Joseph Merrick to the nearly transparent skulls of neonatal rodents. The truly mysterious part is what the framework protects, namely the ball of neurons that can be used for either good or ill. It really is a shame that humans can't lay sole claim to the skull, it being a perfect metaphor for human rationality (affectionately known to herself as 'Here-We-Go-Again-Zen and the Art of the Pointless Question')--with the control center of a creature's life being sheltered by the frame, only getting bits of information fed through a few tiny holes, and still pretending it might possibly have a clue as to what is going to happen next.