Interesting idea, but i dont think its really neccessary to build a 'fretting and plucking machine' :-)
Sure, every pluck of the string results in a unique amplitude and harmonics, but really, the plucking doesnt enter into the intonation discussion at all.
Assuming a properly set 'nut, neck relief, and bridge saddles' - all that is required is simply the ability to fret the note without applying so much excessive pressure as to make the note sharp. Its impossible to make the note flat, its either going to be spot on, or possibly slightly sharp (if you press REALY hard, with tall frets!)
More likely error would be from a slight sideways bending motion, but thats easy to avoid in clinical testing conditions, i would think!
Anyway, for the purposes of a few intonation measurements, i think most bassists are capable of consistently fretting correctly, that is - the minimum fretting pressure in order to have the note sound, without any sideways bending involved.
And since these things are meant to be played by humans anyway, any minute variations in fretting shouldnt amount to enough deviation to warrant a conclusion of BAD APPLE - after all its gotta be close enough when playing music on the fly, anyhow...
I think the human error factors would tend to average and cancel themselves out if enough samples were taken!
I AM glad to hear that after 13,000 instruments have been made, there has been exactly ZERO official reports of an inherent intonation problem. That pretty much puts my mind to rest, thanks :-))