Can't update models inside prefabs?

Unity Engine
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I have an FBX with a character model. I brought it into a scene and did some setup–adding colliders, scripts, setting up AnimationControllers, rigidbodies, and so on. I then created a prefab of it, so I could reuse the character in different scenes, which seemed to work fine.

However, I found that the prefab actually baked most of the character into the prefab. If I go back and update the FBX, eg. adding another object or adjusting a joint, the prefab doesn’t reflect it. I’d have to recreate the entire prefab from scratch.

Reimport FBX and update my character prefab? - Unity Engine - Unity Discussions suggests doing all of the setup in an importer script, which is completely unworkable. (I’m expected to write a script to reproduce setup that took days to get right in the editor? That’s crazy.) I see people talking about it here (with a lot of people who seem as bewildered as I am), but it trailed off with no conclusion and no usable workarounds.

I see Unity Asset Store - The Best Assets for Game Making, but working around this at a script level seems frightening (but I’ll probably try it anyway, lacking any other solution).

Is Unity’s basic prefab handling really this broken?

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Does this work for you: Updating prefabs when its source mesh has changed? - Unity Engine - Unity Discussions

That specific post seemed to find a workaround.

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That seems to just replace that GameObject tree in the prefab with a link to the mesh asset, and not make it so the prefab applies its own changes on top of the objects in the source asset. (For me it just replaced the entire contents of the prefab, leaving me with just a bunch of meshes–the whole skeleton was gone.)