It does raise the question of why the same word would be used in two different ways, one that includes everyone and one that does not. But like a lot of issues dealing with Starfleet enlisted personnel, they made it up as they went along so there are bound to be inconsistencies.
Eh, it's not like real life organizations always use consistent terminology (because of tradition, accident or whatever other reason). Strictly speaking the current system isn't completely logical either. Commissioned officers are officers but non-commissioned officers aren't. The word "officer" is part of both terms. But when used on it's own it's understood that it refers only to commissioned officers. So one could raise the question of why a generic word is used to refer to only one more specific version of it and not to the other.