In axiomatic set theory the term "set" and the relation "$\in$" are primitive notions. Thus, it is not defined what sets are nor what the relation is. Axiomatic set theory is supposed to formalize how sets "behave", meaning what is true about them. One of the axioms is the axiom of infinity, which ensures that one can encode the natural numbers as sets, thus proving their existence from ZFC. This is one common procedure that is done in mathematics: we have an intuitive notion, namely the natural numbers "$\{1,2,3,4,...\}$" that we used for a long time and want to make this precise mathematically. Thus, when ZFC is used as the chosen foundation, one tries to encode this intuitive object using sets.
Another example where this is done is the notion of a function. Intuitively a function is an object/concept of mapping an object of one collection to exactly one object of another collection. This can again be defined in set theory: Suppose that $X$ and $Y$ are sets, then a function $f$ is defined to be a subset $f \subseteq X \times Y$ that satisfies the following condition. For every $x \in X$ there exists exactly one $y \in Y$ such that $(x,y) \in f$. Thus we have proven that there exist objects that we call "functions" that have the property we intuitively expect functions to have, or more precisely that we expect the intuitive notion of function to satisfy.
These are of course only two examples of many, where some intuitive concepts are encoded as sets. In my understanding, we have built "models" (I know this term is used with a meaning in logic, however I don't know if this is the same way its being used there; I am using it with the usual meaning of being a model for somethign) for intuitive concepts. It might be however, that, assuming the existence of mathematical objects, the actual objects are not encoded as sets, or that you are using a different definition for the same concept. In this sense, these might be the "wrong" definitions, without us knowing whether they are or not. My question is, why is this not problematic? Why do we not care what mathematical objects are but only what we can do with them/what is true about them?
An attempt of answering this myself: I suspect that this is because the models we built above satisfy the essential properties we expect the intuitive notions to have. That is, if these intutive notions actually exist, they would have to have these properties. Thus when we prove anything for our models only using these properties, they necessarily would also have to be true for the actual objects. The same goes for different definitions/models of the intended intuitive notion. They would have the same essential properties. Thus, it doesnt matter what the mathematical objects are, since our model serves to prove the properties about them, no matter what they are.
If I understand correctly, a similar view can be found in these notes that I randomly found some time ago. On page 25 of the document it says: "The theorems that we proved for a Peano system also turn out to be true when they are interpreted as being statements about whole numbers. This is just what one would expect: if the axioms of $\mathcal{P}$ are true when interpreted as statements about whole numbers, then all the logical consequences of those axioms (theorems) will also be true about whole numbers."
Another related question: When axiomatic set theory doesn't say what sets are, then could they be anything that satisfies the axioms? One intuitively has collections in mind when thinking about sets, which should be fine, as long as one uses the axioms to construct new collections. However, axiomatic set theory doesn't tell us that sets are collections. They could thus be anyhting. If this were correct, I guess one could use the same approach as above and view sets as a model for collections, meaning that the intuitive notion of a collection obeys these axioms, which means that anything we prove about sets is also true for the intuitive notion of a collection. So are sets necessarily collections?
All of this would also make it a bit more intuitive why abstract concepts such as numbers of pure math actually work when talking counting real world things, or applying these concepts in general to the real world.
Mathematical vs Physical ideas:
For a physical object/ concept, a description / definition of it is a reduction from it i.e: something which may have less properties than the object. This is because the accuracy of our description is limited by the accuracy of senses we have to perceive it. For a mathematical object/ concept, the description/ definition is the object in itself.
For example, when we speak of sets or functions, there is really no object or idea in the world which we are basing referencing the idea with. It maybe that a physical idea inspired it, but the mathematical idea is totally disjoint from any physical motivation it has.
Problems which may arise when going back and forth:
It can be found that many inconsistencies arise when we go from idea in a context to a mathematical idea then try to apply the mathematical idea in a different context of an idea similar to the original. See here.
Are mathematical definitions objective?
I believe even mathematical objects are not free from the limitations of the human mind. For example, how do we know that what you understand from reading a mathematical definition and what I understand from reading that same definition is the same? For discussion on how this issue can be resolved, see here
How does one transition from intuition to rigor?
I found the most insightful section to be in the initial chapter of Terrance Tao's Analysis where he builds up the Natural numbers. Essentially he begins with some basic objects, and some 'reasonable' rules between the objects so that the objects are actually expressive of the conceptual idea of Natural numbers.
It turns out later that we need more axioms to restrain what the objects generated out of the above premises can be, and hence axioms are added till finally the natural numbers defined through this axiomatic way is exactly the type of thing is what we want them to be.