bed levelling is supposed to cope with variances.
imho if you are seeing low spots where you would need to make a manual correction of 0.05 or more there is an issue, for me i see the issue on glass, stock surface and energetic pei surface.
on the stock surface the automatic sensor measures the metal below the sticker, not the sticker - so i guess its possible that the sticker and its glue have different deformation to the metal… you could account for this by doing manual calibration as the reference point is then the actual surface at each point, not the metal beneath it. Have you tried that?
might want to look at this where we are talking about another similar issue
Teaching Tech Calibration Gcode - Snapmaker 2.0 - Snapmaker: where creation happens
personally i have my card one at one stop above tension and i am getting ok results in the center.