I haven't completely investigated entire bone rigs with tracking yet. My initial experiments only involved rotation which caused me to miss the problem regarding perspective and foreshortening and the child bone
chains.
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The following is a "thinking out loud" process that often gives me insight...
From a scripting perspective this issue has to do with "doubled" motion of the bone to it's parent tracking the same point/s.
Turning IK off isn't "fancy" actually. It is the same thing we did ages ago to include the angle offset in the child bone's position. It is exactly the same as Fazek's translate bone tool that allows movement of parent bones without moving the child bones. That is what really causes the issue with motion tracking. The child bone's position is always "0" in relation to the parent.
What is needed to solve this and create an "IK switch" would be to include the parent offset for all the bones in a chain. I already do this with my copy/flip/paste bone scripts. When creating those bones I have to include the offset to the parent. As I said, Fazek's bone translation tool also does this, so the "code" is "out there".
So... the idea would be to have a script that would be controlled somehow (with a button or attribute of another bone) so it includes the offset when doing video tracking. I think the bone control would work best. Move or rotate a special bone and it keys IK off/on.
With IK off, the layer script would key every bone's translation minus the parent's translation/rotation offset. It would actually make the entire rig behave as if all the bones were "root" bones. This would be a simulation of course. From that key foward the script would control the bones rotation and angle if it has a parent. This would be done WITHOUT keys since keys are being placed by the tracking feature.
Probably... this could be done AFTER tracking the bone. So it could be a "button" that you click after you have tracked the bone and created the keys for IK.
Turning IK back on again would key all the bones in their current positions and return the bone behavior "back to normal".
<sigh> more complicated than it sounds.
-vern