Are we talking about the same thing? Mounting plate = webbed undercarriage (‘platform’ in the manual)? Or the plate on each y axis module that the carriage screws to? I see - you said mounting plate for the bed - must be the ‘carriage’ I’ve been referring to it as, or platform in the manual. Yes, it likely was bent in shipping, and being cast metal I’m not going to attempt bending it back.
If it was the plates on the axes that webbing connects to you were referring to, which is a thought I didn’t think of until now, I’ve checked those and they are quite flat, but they could be twisted slightly. That probably doesn’t explain the measurements I took fully, but that would be something to look at for shimming, possibly.
Also, I went to the shop and grabbed my digital angle meter. On the close Z tower the 3 rotations that should be 90.0 degrees are 89.75 (rotate around X), 89.85 (around Y), and 90.35 (around Z). That’s extremely close. I checked the far tower as well and it’s measurements were nearly identical, within .1 degree of all measurements.