That's only true if the player is flying a stock ship. If the player is flying a custom ship, then that technically would be a prototype. :p
When you're using a Rhode Island saucer with a Quasar hull, Aurora pylons and Nova nacelles it is no longer a stock ship. Of course, it also doesn't limit players from simply slapping the registry on a Defiant and calling it good.
Even if you have a stock ship, how many people are also using stock equipment? Numerous ships are flying around with altered weapon layouts, exotic energy weapons, borg bits sticking out every which way, and all manner of unusual equipment, not to mention some of the just plain weird things some of us have sitting around. Borg assimilated tribbles, metal eating lava slugs, and pattern enhancers that give Temporal Investigations night terrors all manage to not be the strangest things in my inventory. I think just about everyone can argue for using NX on their ships except people who are RP purist enough that they wouldn't be using it anyway.