This is an answer to my own question, based on Alex Kruckman's comments. My question was related to another Math StackExchange question ("How can there be genuine models of set theory?"), but I think it was different enough to not be marked as a duplicate.
We can view an axiomatic set/class theory like NBG in two ways. One is as rules for validly manipulating and working with classes. Then, in order to use classes, we just need to make sure we follow the rules of the theory. Another is as axioms for any collection of objects, together with a "membership" relation between them, that satisfies the axioms. These objects need not be sets or classes (in fact such a collection can't have proper classes as elements), and the membership need not correspond to "traditional" set membership. This is just like how a model of $a+b=b+a$ need not be the set of integers, and $+$ need not be addition of numbers. The model theory of a theory like NBG applies to the second usage, not the first.
So there is no contradiction in terms of validity. We can work within NBG and follow its rules to use classes correctly, or we can study the models of NBG just as we study models of the group axioms or ring axioms. Furthermore, models are always assumed to be sets, so this distinction would apply to any axiomatic set theory without classes too, like ZFC (since we can't have the set of all sets.) (We can study proper class-sized models too, but they are then called "class models" or "inner models." The term "model" without qualification is assumed to be a set.)
Another way to look at this is as follows. Sometimes when working say with vector spaces, we call the elements of an arbitary vector space "vectors" even if they're not elements of $\mathbb{R}^n$, which are the "standard" vectors. Similarly, when we have some model of an axiomatic set theory like ZFC or NBG, we may call its elements "sets" in that context even though they are not actually sets in the standard sense. We call a standard set an external set, and we call an element of a model of ZFC/NBG/etc. an internal set. Then, the distinction comes down to external vs internal sets.