The question can be seen as: please explain the apparent contradiction (the paradox) between the answers in Can we express the theory of a single topology as a multi-sorted theory? and in (Why) is topology nonfirstorderizable?. The first answer states "any attempt to 'first-orderize' topology will result in things which look like topological spaces 'up to first-order facts' but are not in fact topological spaces." The second answer states "Virtually all of mathematics can be directly formalized in first-order set theory, and in particular this is how topology is usually formalized". The similar statement "FOL is all the logic we have and all the logic we need." by John Alan Robinson in his paper in computational logic mentioned in this other answer is also relevant.
For example, using arithmetic for simplicity, in Manzano Extension of First Order Logic (p.116), Peano's axiom of induction for arithmetic is expressed in second order logic (with $c$ a constant intended to be $0$ and $\sigma$ a unary function intended to be the addition of $1$) as $$\forall X\,(Xc \wedge \forall z(Xz \rightarrow X\sigma z) \rightarrow \forall x\; Xx$$ In this formulation, $Xc$ has the fixed interpretation $c \in X$. Manzano does not use the symbol $\in$ because its interpretation is fixed in the second order semantic. But there is a problem with this formulation, because it quantifies over all possible subsets of numbers $X$. No calculus can keep up with that much expressiveness. In any specific context where this axiom is to be used to prove things, this extra expressiveness is useless. When we think about proof systems, which we must in practice, we are led to first-order semantics because those semantics satisfy the completeness and compactness theorems. Any sentence that is provable in first-order semantics is also valid in second-order semantics. But not every sentence valid in second-order semantics is provable, regardless which effective proof system we choose. This is saying that in practice, in the context of a practical calculus, we are essentially always using the first order version, which can be stated with the same syntax, but using the Henkin semantic, which restrict the meaning of $\forall$ on the higher order variables. So, all those who insist that we are using the standard higher order formulation (without Henkin's semantic) seem to be ignoring the practical side of mathematics. On the other hand, with the Henkin's semantic, the Löwenheim-Skolem theorem comes back as a true theorem and the non standard arithmetics as valid interpretations. Using this argument, many argue that we need the standard higher order logic. I ask the question, because it's hard not to agree with that other side of the story. The examples provided in the answers below are very convincing. Yet, again, we could also say with Manzano that "second order logic with standard semantics has great expressive power (too much, we might say)". In this analysis, am I overlooking some folk's knowledge regarding logic that would explain this paradox?
Why the answers below are unsatisfactory, but useful: They do not reconciliate at all the answers in the two linked question. On the contrary, HallaSurvivor emphasizes that "there are plenty of properties we're interested in topologically that are not first order". This means that FOL cannot be practically used to axiomatize the class of topologies. On the other hand, the answer of Carl Mummert says "virtually all of mathematics" can be done in FOL. The natural meaning of "virtually all of mathematics" must clearly include topology. So, we need to understand what Carl Mummert means by "virtually all of mathematics can be done with FOL" and how it includes topologies, even though their class is not FOL axiomatizable. The answers do not do that at all. They are very useful answers with examples and I asked these examples as part of the original question. I said that these examples will shed some light and they did, but yet they simply do not answer the question.
There is also no answer to my question in Why is the class of topological spaces not axiomatizable?, which mentions the same paradox and then simply proves and discusses the non axiomatizability of the class of topologies, without really explaining the paradox.
I think I know what is meant by "virtually all of mathematics" so that there is no contradiction and I am just checking that. The idea is that when we translate a statement into a FOL version, we might lose important properties, but the meaning of the statement corresponds to what can be proven with it in the available calculus. It's also that at this proof level, we do not care about the whole class, but about the specific property used in the proof system. This applies also for set theory, number theory and many other theories. Take number theory for example. One can argue that FOL is not sufficient to capture every thing about number theory. Yet, in many applications, it's fine to use number theory defined by FOL. If you need a number theory that is more special, perhaps you can also define it with FOL. In this manner, FOL would be sufficient to do virtually all mathematics and that would not contradict the fact that the FOL statement does not capture the full meaning. This would unify the answers of the two linked questions. This appears to be the simple meaning of "virtually all of mathematics can be done in FOL". Yet, this is not satisfying, because we still need to talk of topologies, etc. in terms of specific higher order standard structures. In that sense, one should refuse to say that essentially all of mathematics is done with first order logic. So, the question is clear. How, do we explain this paradox?