Are you somehow basing that on the fact that the ersatz Dauntless in VGR: "Hope and Fear" had the number NX-01-A, by analogy with the Enterprises being NCC-1701-A etc.?
It doesn't seem like they would make an obvious 'NX-01-A' as anything BUT an homage to an 'NX-01' of Starfleet. Saying that Starfleet's 'NX-01' (likely a prototype cruiser) was the USS Dauntless doesn't seem like much of a stretch to me.
We've seen plenty of Starfleet vessels that reused old names without reusing their registry numbers.
But we've NEVER seen a suffix letter used for anything but an homage to an earlier ship. (Even in the cases where the registry was retconned to a 'regular' NCC registry).
Besides besides, it wasn't even a real Starfleet vessel. It can't be taken as evidence of anything pertaining to the real Starfleet.
I think that knowing what the NX-01 was would be common for crews, even on the USS Voyager. If the name was wrong, the crew would have noticed, right?
You're right about that much. This whole "flagship" nonsense is a regrettable case of fan sentiment infecting the canon.
It was was Roddenberry, really more for TNG than anything else, since he was aping his own 'Starship' bible and scripts for the beginnings of TNG. In that series, the 'perfect ship' was the Flagship of a perfect fleet, with perfect people, and perfect teeth.