There isn't much downside, but it probably involves a small amount of money (paid for the certification) and it means spending time making sure that everything remains 100% within spec. There's lots of little edge cases where BSDs differ from the spec and it means that Apple needs to take care not to drift from the spec.
It’s a spec that doesn’t really matter in practice. Like some other comments said, Linux, BSD and Solaris are “Unix but not Unix(tm)”, and nobody cares.
As pointed out by amiga386 both here[1] and in earlier posts, macOS is not actually compliant with the Unix spec and never has been. This has apparently not been a hindrance for the certification of every single non-compliant version. Unix certification for Apple might not involve anything other than payment.
