I've concluded that this can't be the reason. It'd only result in an error where the size reported by 'du' is smaller than the apparent size (aka number of bytes reported by 'wc -c') of the file. What we see here is that the size reported by 'du' is almost twice as large as the number of bytes. That can't be the result of dedpulication.

I'll chalk it up to "some APFS weirdness".