Lets examine the axiom schema of Separation in ZFC set theory. The formula is
$\forall A \exists x \forall y (y \in x \leftrightarrow y \in A \land \phi(y))$
Now per Godel incompletness theorem, there is a sentence $\theta$ such that ZFC neither prove nor disprove.
Now lets take the set
$\Omega= \{y \in A | y=y \land \theta \}$
Now ZFC proves $\Omega$ to exist via Separation. Also it proves it to be unique (for each $A$)! But what are exactly the members of $\Omega$???
The clear answer is that it doesn't have a clear membership!!! Its membership is model sensitive, i.e., it depends on adding further axioms, so for example if we add $\theta$ to the axioms of ZFC, then we'll have $\Omega=A$ in the resulting system, while if we add $\neg \theta$ to the axioms of ZFC, then we'll have $\Omega=\emptyset$ in the resulting system.
Of course ZFC itself cannot prove either case, nor can it prove $\Omega$ to be neither $A$ nor $\emptyset$ since this would contradict some consistent extensions of it. This means that the membership of $\Omega$ is undecided from the axioms of ZFC alone!
The problem is that $\Omega$ is not even a case of postponed membership, i.e. there is only one kind of membership of $\Omega$ after adding sufficient axioms to clear its identity. No! here even if we add axioms still the identity of $\Omega$ depends on those axioms, so it can differ with different extensions. So we can say that across extensions of ZFC, $\Omega$ doesn't have a fixed identity.
If the above is correct, then what's the rationale from having an axiom schema like Separation if it leads to defining and proving the existence of sets of undecided membership in it? Sets that are vague from its own perspective?
Can't we have a restriction on schemata of ZFC such that only sets with clear cut membership (or at least postponed) can be constructed? i.e. sets whose membership won't change with different extensions of ZFC?
ZFC is really a red herring here: the same phenomenon happens already in, say, PA. For example, PA proves
More generally, we have:
Turning back to the original question, note that Separation need not be used here in the context of ZFC; for example, without using Separation ZFC proves that $$X:=\{\emptyset: CH\}$$ is a set while not determining whether $X=\{\emptyset\}$ or $X=\emptyset$. The way ZFC proves this is by cases: first showing that $\emptyset$ exists, then showing that $\{\emptyset\}$ exists, and then concluding that there is a unique $X$ with the above property.
And $(*)$ applies to basically every reasonable theory - the only way to avoid it is to either go ultraweak, to the level of theories not capable of defining two provably distinct objects, or to go to complete theories which entails either dropping computable axiomatizability or again losing almost all logical strength. So ultimately the answer to your question is: no, not without giving up absolutely fundamental properties of ZFC (namely its strength and its computable axiomatizability).