Continuing the discussion from A snippet to debug font by visualizing baseline, cap-height, etc:
On the topic of baselines in equations, I did some research on this in a previous topic.
Code for the result is here, the short story is that if you drop a mannot-like marker into the equation, it will place itself on the baseline, black circle in the following image:
The colored circles are the bounding box. Once you have a mannot-like marker for the baseline and the bounding box, you can compute the relative distance.

