I'm not an expert in this field, but the way I understand it is that
Choice Trees extend the ITree signature by adding a choice operator. Some variant of this:
ITrees:
CoInductive itree (E : Type -> Type) (R : Type) : Type :=
| Ret (r : R)
| Tau (t : itree E R)
| Vis {T : Type} (e : E T) (k : T -> itree E R)
ChoiceTrees:
CoInductive ctree (E : Type -> Type) (C : Type -> Type) (R : Type) : Type :=
| Ret (r : R)
| Tau (t : ctree E C R)
| Vis {T : Type} (e : E T) (k : T -> ctree E C R)
| Choice {T : Type} (c : C T) (k : T -> ctree E C R)
One can see "Choice" constructor as modelling internal non-determinism, complementing the external non-determinism that ITrees already allow with "Vis" and that arises
from interaction with the environment. (Process calculi like CCS, CSP and Pi, as well as session types and linear logic also make this distinction).
There are some issues arising from size inconsistencies (AKA Cantor's Paradox) if / when you try to fit the representation of all internal choices (this could be infinite) into a small universe of a theorem prover's inductive types. The ChoiceTree paper solves this with a specific encoding. I'm currently wondering how to port this trick from COq/Rocq to Lean4.
And we're not opposed to choice trees. I personally am not too familiar with them but there's time to catch up on literature. :)