This is an edited and improved answer; see edit details at the end.
We can obtain the whole of ZF using a single, natural, scheme.
I will keep the definition of level from Button 2021, as cited above. (The definition needs a slight tweak, because Button 2021 assumes extensionality, but that assumption is easily removed.) Intuitively, our scheme is as follows, for any definable partial function $\tau$. For any $a$, there is a level $s \ni a$ such that: for any $b \in s$, exactly one set in $s$ comprises the $\tau$-images of $b$'s members.
Here is the scheme precisely, with $Lev$ as in Button 2021:
The Main Scheme. Where $\tau$ is any definable partial function, this is an axiom:
$$\forall a (\exists s \ni a)\big(Lev(s) \wedge (\forall b \in s)(\exists ! c \in s)\forall z(z \in c \leftrightarrow (\exists x \in b)\tau(x) = z)\big)$$
To avoid mis-understandings, here is how we might re-state the Main Scheme, in terms of arbitrary formulas. If $\forall x \forall y \forall z\big((\phi(x,y) \wedge \phi(x,z)) \rightarrow y = z\big)$, then
$\forall a (\exists s \ni a)\big(Lev(s) \wedge (\forall b \in s)(\exists ! c\in s)\forall z(z \in c \leftrightarrow (\exists x \in b)\phi(x,z))\big)$.
Theorem. The theory whose only axioms are all the instances of the Main Scheme is a re-axiomatization of ZF.
To prove the Theorem, I will prove a few lemmas.
Lemma 1. The Main Scheme entails Separation.
Proof. Fix $a$ and any formula $\psi(x)$. Let $\tau(x)$ be $x$ when $x \in a \wedge \psi(x)$, and be undefined otherwise. By the Main Scheme, there is a level $s$ with $a \in s$ and some (unique) $c \in s$ such that
$\forall x\big(x \in c \leftrightarrow (x \in a \wedge \psi(x))\big)$. So $c$ is the result of Separation on an arbitrary set $a$.
Lemma 2. The Main Scheme gives Extensionality.
Proof. Reason exactly as before, but letting $\psi(x)$ be trivial. So there is a level $s$ with $a \in s$ and a unique $c \in s$ which is co-extensive with $a$, i.e. $\forall x(x \in c \leftrightarrow x \in a)$. Moreover, if $d$ is co-extensive with $a$, then also $d \in s$, since $s$ is a level and hence is closed under subsets of members (see Button 2021 section 3). So all sets co-extensive with $a$ are in $s$, and hence are identical.
Note: having obtained Extensionality, we can re-write the Main Scheme like this, where $\tau$ is any definable partial function, and where we write $\tau[b]$ for $\{\tau(x) : x \in b\}$:
$$\forall a (\exists s \ni a)\big(Lev(s) \wedge (\forall b \in s)\tau[b] \in s\big)$$
It's worth noting how this resembles Replacement.
Lemma 3. The Main Scheme gives Stratification and Endless.
Proof. Let $\tau(x)$ just be $x$. By the Main Scheme, for any $c$ there is a level $s$ with $c \in s$. Now $c \subseteq s$ (as levels are transitive; see Button 2021 section 3) establishing Stratification. And also every level $c$ has a successor, establishing Endless.
Lemma 4. The Main Scheme gives Infinity.
Proof. Let $\tau(x)$ be $\{x\}$. Using everything we have established so far, $\text{rank}(\tau(x)) = \text{rank}(x) + 1$ for every $x$. By Endless and the Main Scheme, there is some level $s$ with $\{\emptyset\} \in s$ such that: for any $b \in s$, also $\tau[b] \in s$. Since $\text{rank}(\tau[b]) = \text{lsub}_{x \in b}\text{rank}(x)$, it follows that $s$ is a limit level.
Lemma 5. The Main Scheme gives Unbounded. Proof. Let $\tau$ be any total definable function, i.e. $\tau(x)$ exists for any $x$. Fix $a$; by the Main Scheme, there is a level $s$ with $\tau[a] \in s$; now just note that levels are transitive, so $\tau(x) \in s$ whenever $x \in a$.
Combining Lemmas 1-5: the Main Scheme yields LT + Infinity + Unbounded, which is equivalent to ZF (as in Button 2021; the key to that equivalence is to prove, in ZF, that the $V_\alpha$'s are the levels). This final result completes the proof of our Theorem:
Lemma 6. ZF proves the Main Scheme. Proof. Fix $\tau$. Replacement tells us that $\tau(x)$ exists for any $x$. Using recursion, we can show that, for any $a$, there is a level $s$ with $a \in s$ and closed under $\tau[\cdot]$, i.e. if $b \in s$ then $\tau[b] \in s$.
Explanation of edits. In my original answer, I offered a simpler scheme:
$$\forall b \exists c \phi(b, c) \rightarrow \forall a (\exists s \ni a)(Lev(s) \wedge (\forall b \in s)(\exists c \in s)\phi(b, c))$$
This a slight variation of a scheme suggested by Dana Scott (1960, "The notion of rank in set-theory"). The variation is suitable, given my definition of level.
Using arguments like those above (but simpler!), I showed that Extensionality + Separation + the Scott-like Scheme is just ZF under a different axiomatization.
Then @ZuhairAl-Johar suggested the improvement (in discussion below), tweaking the above to what I've now called the Main Scheme.