Of course these so called sarcophagi are the best evidence that the pyramids were tombs but it's still circumstantial and semantic. It's very little evidence for a discipline that claims to have a mountain of cultural context.
Perhaps the box contained the Khufu Library. How in the world do they get from there's no evidence except a box that is known to have sometimes served as a coffin to the pyramid is a tomb? This "evidence" simply exists in a near vacuum of support.
I don't know if anything was ever in the box. This is the kind of question we need actual science to investigate rather than circular logic. I'm sure I could come up with several possibilities of things that the box was intended to hold.
Frankly even if there were a body in it it still wouldn't prove that the pyramid was constructed merely to hold the box which held a body. Egyptology puts the cart before the horse.