Let $T$ be the $\mathcal L_\in$-theory whose axioms are the axioms of $\mathsf{ZFC}$, with extensionality replaced by its negation, and an additional axiom specifying that every set has a unique powerset, formally
$$\forall x\forall y\forall z((\forall v(v\in y\leftrightarrow v\subseteq x)\land\forall w(w\in z\leftrightarrow w\subseteq x))\rightarrow y=z),$$
where $a\subseteq b$ is to be expanded as an $\mathcal L_\in$-formula in the usual way.
Is $T$ consistent relative to $\mathsf{ZFC}$? The motivation for this question comes from the fact that $V\setminus V_\omega$ models $\mathsf{ZFC}$ with extensionality replaced by its negation, but powersets are not unique: for every $x\in V\setminus V_\omega$ both $\mathcal P(x)^V\setminus V_\omega$ and $\{s\in V\setminus V_\omega\mid s\setminus x\subseteq V_\omega\}$ fulfill the definition of powerset.
As Noah commented. ZFC + Ur-elements is known to be consistent relative to ZFC. It is usually referred to by "ZFA", i.e. ZF with atoms. In one formulation of that theory ONLY empty objects violate Extensionality! So we do have many empty objects (the Ur-elements). However all non-empty sets are extensional! That is, "No distinct non-empty sets are co-extensional (i.e. have the same elements)". Clearly this theory satisfy all of your conditions.