I think I just factually disagree with you here. I think it would be very rare for a fluent English speaker to hear “cradle of civilization” and need to actually do the work of calling up the concept of a baby bed and make educated guesses about what metaphorical similarities the speaker is trying to evoke.
In fact, in American English I think it’s pretty rare to use “cradle” in informal speech to refer to a baby bed. “Crib” or even “bassinet” or “baby bed” are much more common. “Cradle” is in the lyrics of a well-known lullaby, but to use it in casual speech would be somewhat conspicuous. It’s much more common as a verb, like “cradle the baby in your arms,” which I suspect you would also describe as a metaphorical usage (and I would disagree).