question

Since FlexSim allows you to freely code logic or even connect to external code (for example to use a premade Python library) I would say there is generally nothing that's outright impossible. It's all a question of how having the time to learn and implement the logic you need.

For the three you mention:

Put-to-wall is relatively simple. It would involve reserving a slot in a rack for items from a given order and routing all items from the picking process there.

3D Shuttles are a bit harder I'd say. You need to think about the underlying data structure that represents the slots in a 3d storage, since the build-in storage objects only really deal with two dimensions. The movements of the shuttle are not too complex.

(When you say AMRS 3d shuttle I think of a system like seen below. If you mean something else, then it might of course require other considerations).

I haven't personally done much in the way of collaborative robots yet. But maybe the linked post (while a somewhat different topic) is a useful example of the possibilities of FlexSim.

https://answers.flexsim.com/articles/136679/optimized-agv-dispatching-with-google-or-tools.html