As far as I know, the main difference between :is() and :where() pseudo-classes is that :is() takes the specifity of the most specific of its elements, whereas :where() has a neutral (zero) specifity.

From my point of view, the zero specifity if what we need more often, and this is why it seems that when either :is() and :where() can be used, it is better to use :where(). Practically, there will be no difference, but why use tool which is designed for a slightly different use cases then yours?

(This is the same reason why prefer :nth-of-type() over :nth-child() when either of them can be used: there are very rare cases when you can use :nth-child() but not :nth-of-type(); whereas there are very few cases when you can use :nth-of-type() but not :nth-child(). That is, we can say that :nth-child() is a more niche thing, like a truck compared to a car.)

But then, why user agent style sheets prefer :is() over :where()? For example, from the Safari for Mac user agent style sheet:

:is(dir, menu, ol, ul) :is(dir, menu, ul) {
    list-style-type: circle;
}

Does it mean that, to put things simple, my reasoning is wrong, and when either :is() and :where() can be used, it would make more sense to use the former?