I've said it before, and it bears repeating here: ContentID is not, has not been, and will never be the DMCA. It was developed by YouTube so Viacom would drop the suit that would likely have stripped YouTube's safe harbor protections under the DMCA. ContentID takedowns are not DMCA takedowns. They operate on a different, much less strict standard. Anyone that works with YouTube can flag any video for any reason (see…
Which suggests a nice solution if Congress were to be reasonable: amend the DMCA to clarify that ContentID itself would invalidate safe harbor. In other words, require actual neutrality for safe harbor.
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.