Although people often talk as though it just doesn't matter which approach you use — perhaps all universes are alike? Let me prove that in a strict sense this is not true. The nature of the mathematical setting that arises is necessarily different in the various accounts, different in regards to some core foundational issues in category theory. All universes are not alike, and perhaps none of them is like the proper class category, even with respect to first-order internally expressible features relevant for category theory. It is never the case that all universes have the same internal theory as the full universe $V$ or each other, although it is possible that some of them do. In this sense, yes, there are substantive differences; and no, they are not "the same."
Suppose we place ourselves at first in an ambient set-theoretic background of ZFC with unbounded many inaccessible cardinals, that is, where the universe axiom holds. In this case, the category of sets considered as a definable class will have the property that it thinks there are many Grothendieck-Zermelo universes inside it, and, in particular, every set exists in such a universe. In short, the existence of all those inaccessible cardinals is observable inside the category of sets.
But this is a feature that is not true in every Grothendieck-Zermelo universe itself. For example, if $\kappa$ is the smallest inaccessible cardinal, then the category of $\kappa$-small sets will not have any GZ-universes inside it, a strong failure of the universe axiom relativized to that universe. The next inaccessible will have exactly one universe inside it, and it will think that not every set is in a universe. The category of sets made with the $\omega$th inaccessible cardinal will think there are infinitely many GZ universes, but still bounded in the cardinals, since the $\omega$th inaccessible, being regular, is not the limit of the first $\omega$ many inaccessible cardinals.
If the ambient universe has a proper class of inaccessible cardinals, but no inaccessible limits of inaccessible cardinals, then the background universe (category of sets as a proper class) will think that every set can be placed inside a universe, but none of the universes themselves will think this is true. In other words, in this background, the universe axiom is true inside the category of sets using the class approach, but not when using any particular universe.
In general, knowing the universe axiom is true doesn't entitle you to know that it is true inside any particular universe.
In my paper with Robin Solberg, we investigate the extent to which the various Grothendieck-Zermelo universes admit categorical characterizations — these are the universes that can be characterized by an internal feature, expressed either by a first-order sentence, a first-order theory, a second-order sentence, or a second-order theory.
If there are more than continuum many inaccessible cardinals, then many of them must have the same first-order theory, since there aren't that many theories, but never is it the case (assuming there are at least two) that all universes have the same theory, since the smallest one thinks there are no universes but all others think there are some.
It is possible that some universes have the same first-order theory as the full universe $V$, and this occurs when $V_\kappa\prec V$, that is, some universe is an elementary substructure of the full universe. This is a large cardinal axiom with the same consistency strength as ZFC+"Ord is Mahlo", which is strictly weaker than the existence of a Mahlo cardinal, which is itself a rather mild large cardinal axiom.
Indeed, one can arrange a proper class of inaccessible cardinals $\kappa$ with $V_\kappa\prec V$, and all such universes will have the same first-order theory as $V$ itself, even with parameters. However, it doesn't follow from this that these $V_\kappa$ are themselves models of Ord is Mahlo, since if there is one then there is a least one and perhaps we were already inside that least one, in which case none of the universes below model that theory.
There could be universes $V_\kappa$ that have the same second-order theory as the full universe $V$, simply on cardinality grounds, since there are only continuum many possible second-order theories, and so if there are more than that many inaccessible cardinals then two of them will have the same theory and so we can cut off at the second one to realize that situation. (And these second-order assertions are relevant for category-theoretic assertions such as the existence of functors of certain kinds.) This is a kind of argument that Robin and I use a lot in our paper.
I won't speak about whether these differences will be of interest to category theorists, and perhaps they don't matter much in the practice of category theory. To my set-theorist way of thinking, however, the differences I mentioned revolve around the foundational uses of universes in category theory, and in particular, the subtle differences in how the universes themselves view the nature of the universe axiom and its failures, and so the properties strike me as fundamental, even if most applications are not affected.