Apart from the notion of formal theory, which formalises the idea of axiomatic system in first order logic, in mathematics people also consider another type of axiomatic systems, which can be described as extensions by definitions of the axiomatic set theory that a mathematician uses in his work. The examples of such systems are
etc. As far as I know these are not formal theories in first order logic, although, of course they can be presented as such theories, since they are extensions by definitions of ZFC; I think however that this will be too bulky, so I believe, there must be another notion of axiomatic theory in mathematics, which covers the theories from my list.
Is that true? Can anybody enlighten me if the second kind of axiomatic systems has a formal definition (different from the phrase "extension by definitions of ZFC", so that this indeed clarifies the picture)? Or, in other words,
is there a common scheme that describes the axiomatic systems of second type and explains the differences between them and the formal theories in first order logic?
For some time I thought that these are just axiomatic theories in second order logic, but now I got some doubts, and I would prefer to use first order language for describing the differences (I believe, this is possible).
Generally mathematicians when doing mathematics (like topology, probability or geometry) do that in the framework of set theory.
This means that they introduce some definitions (topology, $\sigma$-algebras, points etc) in terms of sets and provide proofs of facts about these objects using properties of sets.
Formally what mathematicians do is take ZFC theory add new symbols to the language (for instance predicates like "is a topology", "is a topological space", "is a continuous function" and so on) and then axiomatically define these predicates in terms of formulas in the language of ZFC, that is they add some axioms of the form $$x \text{ is a topology} \iff \varphi(x)$$ $$x \text{ is a topological space} \iff \varphi'(x)$$ $$\dots$$ where the formulas $\varphi(x)$, $\varphi'(x)$ etc are ZFC formulas.
In this way they can reduce any proof about the new introduced objects (toplogical spaces, geometric figures etc) to a proof about sets, that is a proof that ultimately relies on the axioms of ZFC+the definitional axioms for the new predicates.
On the other hand in principle one could try to look at the formal systems you listed as some logical systems on their own.
For instance Hilber's system for euclidean geometry can be easily seen as a first-order theory, as it is basically shown in the wikipedia link you gave.
The other systems you listed could be seen as formal systems for an higher-order logic, but you have to go at least third order because in these systems you would need to quantify over families of subsets (that is over families of predicates, or predicates of predicates).
If you like I could add the details, at least for one of the systems. Let me know if you need any additional clarification.
Hope this helps.