This question follows up on a discussion elsewhere at MSE where it was suggested that some set theories do not allow arbitrary separation, while admitting the existence of a universal set.
I have been working for some time with a set theory that allows for arbitrary separation (creating subsets of another set). It is a trivial matter to prove the existence of, for example, the identity function $f(x)=x$ on a given set $S$. Just take the Cartesian product $S\times S$, and select the subset $f=\{(x,y)\in S\times S: x=y\}$. Then, of course, you would have to prove that $f$ is a function. How would this be accomplished without initially invoking arbitrary separation as here?