To put this topic to bed would require someone to creating a ball release mechanism (inlane or straight drop on flipper), along with a ball sensor (opto?) that detects the balls position over the flipper and hook that up to the flipper input. Similar to the Thing flips set up but the opto reads over the flipper somehow.

If the Williams machine hits the ball to the same spot over and over again, while the remakes shot location varies, then there you have it.

I will make this device and provide a video of the results unless PPS promises their next release is a Capcom King Pin remake

Because, if the randomness you are concerned about doesn't manifest as anything significant (ball route doesn't significantly change when delay is introduced), then the discussion is moot.

If you can get the Williams hardware to hit a shot consistently, but then you hook up the BeagleBone to the same hardware/playfield and the shot starts varying, then the only variable introduced that would be a factor would be the BeagleBone controller.

Actually, third party proof that shot accuracy is affected is important. Otherwise, the manufacturer could just say "We tested it internally, no significant issue, it's in your imagination, carry on". Because fixing this would actually cost money, and they have no incentive to put themselves in that position.