Errr,,, Now I am a little busy in other personal stuff (my sons are 15 days in vacations with me... mmm
very busy really) so for the moment I only am reading the forum to not loose track on the posts. None further developments although I am very eager to take up again the researching.
Regarding to where store the x,y,z information It was something that I though also in the past but abandoned it.
Let me think about it out loud and see what can we conclude.
1) You want to eliminate Rx, Ry and pt bones.
2) It is not possible to eliminate the central bones of the limbs because its name is connected to the mX and mY bones that makes their individual rotation. It also represents the center of rotation so its position define the center of the model (or the limb).
3) The parent ship of the points of the limb (that previously was done by the parent ship of the pt bones to the central bone can be substituted by the value "parent bone" of each point. "A point belongs to the limb that its (central) bone parent belongs to" That's a good point (if you forgive the repetition

) for the future 3D rig

4) To store the x,y,z of every point we can use some kind of array similar to the current for TboneSets. It obligate to maintain the points of the side view available all the time. That's not a problem. Also to assure that it is always available it can be calculated in every embedded script call. Same than current design.
Conclusion. It is possible!!!! The amount of bones would be reduced drastically!!!
Let me state some rules (if you don't mind) over some ideas on the fly about this...
1) Draw a model (it could be front or side view or 3/4 or what ever) lets call it original model.
2) Based on that model draw (moving points) your front and side views in each separated layers. Lets call them front and side models.
3) Based on front and side models the user make a 3D rig of the original model. The names of the layers of the original, front and side models should be consistent (face, face.fr, face.sd for example) It would be needed for the script to select the original model layer to move it on the fly. That 3D rig would need masterX and masterY bones and every eventual mX and mY bones and its corresponding central bones of the limbs. In one model without any limb it only would be needed 3 bones. A central one and the masterX and masterY bones.
4) Once you have rigged our model you can animate it with the masterX, masterY and mX and mY bones (and fov and master TR bone for sure!)
5) ALSO ( and you now would understand why have tree layers) You can morph your model just moving the points locations of the side and front models!!! That was one of the reasons for what I discarded the no bone idea!!.
More features!
Now masterX and masterY can be deprecated! We need only mX and mY bones!. In this way it is possible to have more than one model in the same vector layer (bone layer)! It would be VERY interesting because the current design loose some interactivity with the 3D models. Imagine it! now you can have two models (3D characters) in the same layer and sometimes one is above the other and sometimes is behind!. All the work is only done by the sort shapes script!!!
BTW the short shapes script would work the same because finally the Z value is taken form the points and not matter if the z value is attached to a bone or to an array.
Ouch! I have no time
now to work on this!!!

Also I've planned to make a trip the last week of July!!
If you feel brave to write the script please don't hesitate to do it. Although I would be very happy if I could do something.
In August 1st I'll be 100% on this stuff...
But before start witting the behavior of the model should be better defined. My recommendation is this:
First create the model by hand and modify the 3Dgrid script to make the magic.
When it works perfectly (included limbs) then modify the auto 3D rig scripts and the sort shapes script. I predict that the auto 3D rig script would be useless finally. We would use the standard bind points and re-parent bone tools... Only the shape sort would be necessary.
This is exciting!!!
-G