After reading the EFF's letter a little more closely, I realize now that it wasn't even a formal DMCA counter notice representing the repository owners, just an informal legal rebuttal of the original claims. Oops. So GitHub wasn't legally required to restore access at all even after 10-14 days, since no official counter notice was ever received.

That makes it more significant (not merely symbolic) that GitHub chose to short-circuit its DMCA process to restore access and open themselves up to liability in this case.