Morning
@Moderatemixed. I read your previous post and I am also seeing this one here and man you are definitely working with some equipment most of us will never touch in our lifetime. With that being said you may not find anyone here with that particular knowledge ad experience - although I'd love to be proved wrong.
There are other places which people geek out over metrology. When I worked in the industry, I spent a lot of time there getting up to speed. You may find information in those places as well.
www.qimtonline.com
Metrology - Calibration, Gage and 'How to Measure' (and related) questions.
elsmar.com
In addition, other machinist forums (not to be named) have pretty active metrology subforums. You may find help there.
So here is my analysis. An autocollimator detects angular misalignment in yaw and pitch relative to the target, but not roll. You could develop an instrument to mount the autocollimator on two round feet, maybe 1" in diameter, 6" apart. These each would bridge any topography under them, somewhat like a scraping flat. The would need to be ground and lapped extremely flat.
Then manipulate the unit to take measurements, rotating about the table surface to find a measurement minima (removing the yaw component of the measurement, leaving only pitch, the topography of the surface). This, compared to a reference zero, gives the relative elevation between the two pads. You would need to walk this instrument across the surface, taking angular misalignment (over a known span = vertical misalignment) measurements. Then move the setup and repeat in the other axis. Eventually you should be able to build a mesh of the surface with incremental displacement measurements from your zero point.
But I've never done this, so just speculating.