ContentID is more acceptable to the only potential litigants against whom Google would care about the DMCA safe harbor against than is the process which makes available the DMCA safe harbor, so that wouldn't matter.

A safe harbor is a protection against legal liability which you otherwise might have. If you have a separate arrangement which is both lower cost for you to operate and more acceptable to the only people against whom you are concerned about using the safe harbor than the actual safe harbor process, you don't care about a safe harbor.