Good point and important distinction- not to say that courts holding the 'nexus' position have already established Section 512 protections for Section 1201 violations, just that I could imagine a legal argument extending the position along these lines. If Section 512 protects services from liability for user-provided software that contributes to copyright infringement, it should also protect services from liability for user-provided software designed for the circumvention of technological measures protecting copyright infringement.
At the very least in the absence of further clarity, it makes sense that GitHub seems to apply section 512 law consistently across Section 1201 claims in addition to copyright infringement claims, not only to simplify their legal procedures but also to leave such a theoretical defense available to them in case they ever need it.