I have been giving this a ton of thought. I may have a solution for the build plate issue.
First and foremost, powder coating is not uniform on many surfaces. Depends on how it was put down and the grounding used; this means the edges of the plate could be thicker than the middle. Using the textured plate *MAY* be the issue.
Textured plates are very coarse, while smooth plates are flatter. If the textured plate shows as uneven with a ruler, what would a smooth or semi-smooth plate show? You said on the podcast that the bed was flat, but the sheet was not. This could also make the magnetic sheet not flat, in which case you could add something to smooth it out, like a leveling compound. Which, in turn, would make the build plate flat. Depending on the amount and volume used, this may affect the magnetic part, but you can add it to key areas to build up.
It is also not unheard of to use build plates that are smaller or larger than the bed, provided clearance permits it.
So,
Some build plates are not the same thickness throughout. I have a thickness gauge for powder coating that also reads anodizing. Since you probably don't have one, put the build plate on a flat surface (make sure the ruler reads flat on that surface first), then put just the flex plate on it and read it to find the low spots, and mark them to fill in later. One possibility is that the build plate itself is not flat.
If the sheet is flat, it must be the magnetic foam sheet; in that case, you could sand the high spots and/or fill the low spots. You can use a variety of materials, such as filament, tape, and resin, to make it flat.
Since I do powder coating, I am including some PEI powder from my shop for reference on how it looks before spraying and baking.