I think all they are trying to say is your ship needs to have a 6-digit registry
But why? Really doesn't make sense.
There are so many ways to allow lower digits - from (optional?) pre-determined numbers that could even be unique in the entire game and can be "transferred" between a player's ships (using the -B, -C, etc. suffixes) up to just blocking out the ones that are reserved by canon vessels.
Valias, CBS reserved all the lower numbers to prevent any collision/confusion with any future Star Trek developments from them. This is likely the end of the story. I seriously doubt they'll ever let us use numbers below 90000.
My Sovereign/Noble hybrid has a 6 digit registration number. It was assigned a new(and therefore recent and 6 digit) one when it was cobbled together from two damaged ships - such things are necessary in times of war. The registration number is my subscriber number: NCC-347076-F Quantum Flux. F as it's the 5th ship to wear the registration number. Not very canon, but it sits fine in my mind. And at least my ship's not called Enterprize.