I can explain the thinking behind the design, @burnandreturn, and how it works today.
You can think of Joint Origins as an "joint connection interface" to a component. Basically a "put joint here" marker. When you move a component, you want the joint origin to move with the component. And, you almost certainly want Joint Origins to appear in every instance of that component (every instance has the same interface for joints). As such, they are owned by the component that owns the geometry.
Right now, Fusion does not let you make design edits to referenced components. Just as you cannot add a fillet to a referenced component (while editing the top-level design), you cannot add a joint origin. You have to open that design, and insert a joint origin. This is the approach I would take if I needed a Joint Origin in a referenced component.
Now, admittedly, we could change Fusion to allow you to add a Joint Origin to the top level that references geometry in a referenced component. I don't even think it would be that hard (famous last words...). We just haven't done that yet. Joint Origin is seen as kind of an advanced workflow, and most designs can get by without this capability. So, it just hasn't risen to the top of the priority heap yet. As you know, we have lots of requests for functionality. Not to dismiss this one, but I believe that you may be the first one to request it. I did not find it in a quick Idea Station search, and I can't find a mention of this in the forum.
Also, coming at some time (no promises when...) we want to allow in-context editing of referenced components, which will also help here.
Jeff Strater (Fusion development)
Jeff Strater
Engineering Director