One can very well believe that there is absolutely no such thing as any truly uncountable collection in terms of size, while believing that there are uncountable collections in terms of complexity. This might seem crazy, but it is not. If you assume Z set theory (or much less), then indeed there is only one notion of countable, because the other notions are equivalent to it. But if you use a different foundation, then there might be at least two distinct notions:
(1) Countable: S is countable iff there is an injection from S to ℕ.
(2) Weak-Enumerable: S is weak-enumerable iff there is a partial function on ℕ whose range contains S.
(1) expresses countability in terms of complexity, because S may be so complicated that there is no way of distinguishing members of S in order to have an injection from S to ℕ.
(2) expresses countability in terms of size, because if S is truly no bigger than ℕ then we can weakly enumerate it in the sense of adding each member x of S to our enumeration whenever we figure out that x is indeed a member of S.
Again, note that (2) implies (1) in typical set theories, because of their way of expressing "partial function". But it may not in other foundations!
In a foundation with intrinsic partial functions, we might be able to prove that ℕ→ℕ is not countable (1) but be unable to prove that it is not weak-enumerable (2), and moreover the intended model for that foundation may very well be weak-enumerable! The reason is that, if ℕ→ℕ is weak-enumerable witnessed by a partial function F, then we cannot construct an injection G from ℕ→ℕ to ℕ by defining G(h) to be the minimum k∈ℕ such that F(k) = h or 0 if no such k exists, since "∃k∈ℕ ( F(k) = h )" is not boolean and so G would be merely a partial function.
In this foundation, Skolem's paradox is practically gone, because the paradox arises from the idea that uncountable collections are strictly bigger than countable collections. But as mentioned above, ℕ→ℕ can be smaller than ℕ (2) but still not countable (1). Although we should not assume that the world is weak-enumerable, it would be consistent to do so, and in that viewpoint every collection (including every model of ZFC) would not be larger than ℕ. So it is completely unsurprising that a model M of ZFC can be countable; it just means that M is simple enough that there is an injection from the domain of M to ℕ! If M is too complicated, then M is not countable. But in this viewpoint it is always the case that M is not larger than ℕ!
Many of the above points also apply to analysis of Skolem's paradox from a conventional set-theoretic viewpoint. But I mention this viewpoint because you need to realize that your notion of countability is very much dependent on your foundations, and splits into at least two notions in some foundations. In particular, (1) is certainly not absolute. But if your foundational meta-system MS is like above plus an axiom that every type (including the universal type) is weak-enumerable, then MS trivially can prove that every model of MS is weak-enumerable, and every model itself also thinks that its universe is weak-enumerable. Whether you believe this kind of MS or not, countability in the form of (2) is absolute in it!