As far as the quench discussion, glad to see no attempt to make it too tight. I think for most .040-.050 is plenty for the squish benefit, and I regularly run them proud with a 8554 and some even taller if we are trying to keep intake dimensions on the rare stuff. Even comparing .045 or so to .036 I'd expect no gain and only added risk.
In terms of the machining, geez Howie, Brent was right, said Ford was all over the place, and then you come back with Ford couldn't hold a spec with their tech at the time, that is EXACTLY the point. Who cares what the spec is if the machine can't hold it anyway? Brent didn't say that the machinists were evil or FOMOCO was playing a trick on us. I'll add that valve centerline, bore centers, cam bore dimensions are all over the place too once you start measuring.
Additionally, no doubt things flex with heat cycles, I am not sure what you mean by massive flexing, I don't agree with that, an FE is pretty forgiving on head gaskets even fewer head bolts than modern engines. Although anything can move, they don't change .026 from end to end and grow .010 over deck height. That's a crank centerline or deck machining issue that causes that much variance, and the numbers can tell you which it was.
Square deck a block or two, you'll see things, square deck 20, you can really see the trends.