My understanding is the MAC is citing an alleged unwritten rule that was not universally known or agreed upon. Hence their delay in protesting. If it had actually been well-known and agreed upon, they would've been on top of it.
As to the NCAA, they are effectively creating a new rule/protocol, not citing an old one. This is a Bush Push situation. The obvious underlying rationale is that even when the televised clock is the least accurate info available, sticking with it will prevent tens of millions of people getting their panties twisted.