For every c.e theory $T$ extending KP (Kripke-Platek) with a model $M$ of height $α<ω_1$, the intersection of all such $M$ is a subset of $L_{α^{+,\mathrm{CK}}}$. This holds since the existence of such $M$ is $Σ^1_1(α)$. Every model $\text{ZF}+0^\#$ (or just $\text{KP}+0^\#$) of height $α$ includes a set outside of $L_{α^{+,\mathrm{CK}}}$, so such theories do not have unique models for countable $α$.
The interplay of uniqueness and non-uniqueness — and the conditions to guarantee uniqueness — is an important theme in inner model theory. Theories such as $\text{ACA}_0$ or the primitive recursive set theory have unique minimal $ω$-models, but then for c.e. theories extending $\text{ATR}_0$, the intersection of all $ω$-models (if there are any) equals HYP. (HYP is the set of hyperarithmetic sets; it corresponds to $L_{ω_1^{\mathrm{CK}}}$, the minimal transitive model of KPω.) With $0^\#$, uniqueness of minimal transitive models fails. And going further, $L[M_1^\#]$ does not satisfy $V=HOD$: Despite being an inner model, $L[M_1^\#]$ lacks sufficient closure to iterate and identify the true $M_1^\#$ (the sharp for a Woodin cardinal).
Back to the question, for every ordinal-categorical (as defined in the question) c.e. theory $T$, all transitive models are constructible, and for a model $M⊨T$ of possibly uncountable height $α$, $M⊂L_{α^{+,\mathrm{CK}}}$ (uncountable $α$ can handled using countable elementary submodels). Thus, if $On^M$ is a cardinal (and $T⊢\text{KP}$), then $M ⊨ V=L$.
Surprisingly, however, we have the following, which adapts Farmer Schlutzenberg's answer to my recent question Minimum transitive models and V=L (the discussions in the two questions complement each other).
Theorem: There are ordinal-categorical c.e. theories extending $\text{ZFC} + V≠L$ that have arbitrarily large transitive models (assuming ZFC has arbitrarily large transitive models).
Proof: To get such models, we use existence of (non-trivial) $≤κ$-closed forcings with (as viewed from the generic extension) unique generics. Ordinarily, we might have $V[G]=V[G']$ (which interferes with defining our $G$ in $V[G]$), but we can get unique generics by encoding $G$ into choices for subsequent rounds of forcing and iterating $ω$ times (with full support). Next, for every ordinal $κ$ (including uncountable $κ$), the minimum transitive model $M$ of ZFC of height $>κ$ is pointwise definable with ordinals $<κ$ as constants. Fix a formula picking a $κ$ (as above) in $M$, and a parameter-free definable forcing as above. Using the pointwise definability of $M$ (with ordinals $<κ$ as constants) and the $≤κ$-closure, every dense open set has a parameter-free definable (in $M$) dense open subset. Thus, we can fix a choice of the generic $G$ using a computable schema as in the linked answer. Specifically, enumerate formulas; if a formula $φ_0$ defines a dense open set here, then pick its first element (under some fixed parameter-free definable well-ordering), and then repeat with $φ_1, φ_2, ...$, picking the first element compatible with the previous ones. Our theory will be $\text{ZFC} + V=M[G]$ with $M$ and $G$ as above.
A remaining open question is whether there is an ordinal-categorical theory $\text{ZFC} + A + V≠L$ (with a transitive model) where $A$ is a single statement. A model of such a theory cannot be obtained by set forcing (unlike a schema, a statement in the generic extension would be forced by some condition in the poset), and so may require new (perhaps, still forcing-like) construction methods.