I’m a bit wary of having some sort of algorithm determine control over access and classification of parts because that can very easily lead to situations where certain attributes of the player are classified as items that aren’t desired. But this can be easily remedied by just having said algorithm give the option to classify rather than automatically converting the part.
I think I’d prefer “joints” just because it provides greater function to define “limb/not-limb” progression to something that has to do with the underlying presence of or lack of a skeletal structure. Musculature can be really diverse and confusing structures across metazoans as a whole, while “skeletal structures” are a bit easier for the player to wrap their head around imo. Certain capabilities being locked behind the fact that a player has a hydrostatic, exoskeletal, or endoskeletal structure would be more intuitive than muscles.
Joints I think would also allow us to better define diverse abilities attached to limbs. Would a wing be defined by a different muscle? Would a wrist be defined by a different muscle? I can see it being possible, but a “joint” provides us with a more general applicability I think.
To me, I think the appendage in the original concept is basically adjacent to the “bump” in this concept, in that an appendage just starts as a lump of mass too.
You did put more focus on the progression of an appendage into something more functional than the original concept however - your threshold concept brings up interesting questions, and though I don’t think the editor should automatically define what a structure is and isn’t, there is something there. I think it connects to Rathalos’ early point about muscles too:
Where the point is brought up that limb progression needs to be thought of more in-depth.
I think if we put more thought into the threshold system, we can find something really cool that unifies a lot of the remaining questions and design questions related to appendages, limbs, etc.