Completely out of nowhere, but I wonder if the implied meaning is that Kirk & the crew aren't the 1701?
Different universe. A later NCC-1701 built. What if this Enterprise isn't the Enterprise?
What if there were another, that got lost and whose fate was a mystery or a classified secret.
Afterwards instead commissioning a starship with the -A suffix, they gave the name to another ship and pretended nothing ever happened.
It's a bit Babylon 5 meets Titanic/Olympic conspiracy sure enough.