Model translation does not update if model is in any kind of prefab

I think this is "by design", if a bit unfortunate. Explanation on what's going on below. Strangely enough, I haven't ran into that particular problem myself yet -- maybe because most of the time I import models one by one from a 3D app, instead of whole hierarchy of them. Or if there's a hierarchy, then it's for "static geometry" that does not need turning into a prefab.

Now, what I think is going on:

In Unity, there's really no difference between "FBX file" and "a prefab". Both are hierarchies of game objects with components stuff (mostly meshes materials) attached to them. Another thing: in Unity there's no dependencies between any kinds of assets -- no asset can depend on the state of another asset (i.e. there's no way to know that "hey if that fbx file was changed, then these other assets need to be reimported as well").

So what happens is:
1) you import the fbx file from a 3D app - let's call this A. This results in some meshes, and some game objects with their transform positions etc.
2) you drag that into the scene; the objects in the scene know "hey I'm coming from prefab (just a model file here) A, and these are the properties I have changed from whatever is in the prefab". Right now nothing is changed compared to prefab, except the position of the root game object.
3) you create a prefab out of the same thing - let's call this B. Critical thing here: that prefab's game object hierarchy transform positions etc. are completely separate from the original fbx file A by now. They just don't know anything about each other anymore - there's prefab A and prefab B only. Some things are shared however - namely meshes materials (but transforms their data is not).
4) now you put prefab B into the scene. The game objects of this in the scene know "hey I'm coming from prefab B".
5) you change original model file A to move some objects around.
6) A's instance in the scene changes - since the positions come directly from this prefab. But B is a completely separate prefab! It does not even know it came from A file; it has positions other component data as it they were set when you created it.

So... that's what's going on. And yeah, for this particular workflow that's a bit unfortunate.

I'm not even sure how people work around it TBH. Maybe they don't do it? Or maybe they don't create additional prefabs, but instead make all extra components scripts be attached directly to imported prefab A (using AssetPostprocessor.OnPostprocessModel)