I was thinking about this issue. What does the AF confirm chip do in conjunction with the camera AF system?
This is what I understand: When I am mounting an EF mount lens (from any manufacturer) on my canon camera, the processor of the lens lets the processor in the camera know, through the electrical contacts on the mount that a specific lens (focal length, max aperture, and lens ID) has been mounted on the camera. The programmable AF confirm chips also probably do the same thing (at least upto this point). Let's call it the lens id stage.
Now, when I am trying to Autofocus an EF lens, there is again an information exchange between the camera and the lens, which activates the lens AF motor to engage the focus elements of the lens (let's say we have chosen the center focus point only). When the split image on the focusing sensor at the base of the camera reaches a certain level of phase based difference/clarity (or whatever that is called technically) the AF point inside the viewfinder lights up and beeps. So my lens has acquired focus. The same thing happens while manually focusing the lens, except that the lens motor does not operate. Let's call it the focusing stage.
Now, then, what does the AF confirm chips do for non-EF lenses during this focusing stage? The chip has electrical contacts to complete the lens ID stage, but in the focusing stage it has nowhere to take the focusing information to take (as there is no focus motor in the lens). But still the focus points light up and beep when we gain focus. If the mount for the non-EF lens does not have any focus confirm chip then this beeping and lighting up does not happen. Does that mean, for the focus system inside the camera to work, we just need the camera to know that there is some "particular" lens mounted on the camera? So we just need to complete the lens ID stage. For non-chipped mounts the camera does not know that there is any lens at all on the camera and so the focus system keeps on "sleeping". Is that how the thing works? Any clarification is welcome.