Oscalon wrote:what happens if the join helpers themselves are changed? If you scale them, or let them be grabbed by proportional edits, they will be slightly squished or stretched. Does this matter?
No. You might notice that some other MH targets stretch the helper cubes as well.
For calculating the joint position, we simply take the average of the 8 vertices of the cube, or in other words, we use the center of the cube. It doesnt matter if it is twisted, as long as the average position is where you want the joint to be.
Oscalon wrote:How exactly is the helper geo even detected and used? Vertex index?
It's referenced by the vertex indices.
Oscalon wrote:Are the eye, eyelash and teeth geometries that come when you load the base mesh from maketarget in blender essential to maintaining vertex count?
Yes and no. The body vertices come first, so if you remove the helpers you are still able to make targets for the body.
Then come the joint helpers and the helpers for eyes and eyelashes. Finally clothes and hair helpers. You can make targets on any level of granularity, as long as you include the levels under it, so that the vertex indices are kept.