The theoretical explanation does not take into account size of any of the optics. It is a fact of beam dynamics, and can be limited or enhanced based on the real life environment that it is in. Some of the larger range of motion systems, and some of the systems that use different lasers, will use a collimator and apertures to minimize the beam divergence over distance. I believe Epilog has used what the market as Radiance optics on some of their systems. ULS uses a "telescope" or collimator on the HPDFO assy. to achieve a smaller focus diameter across the range of motion of their systems.
I don't remember Lee mentioning anyting about the thickness of the material he is cutting. He just stated that he seemed to get more efficient cut through, the further he got from the beam source. He also said his table was level to the motion system and alignment was pretty close. I offered up a theory that might help explain what he is seeing. It might be something as simple as he gets better air flow or air assist as his laser processing moves from area to area on his system. Without having the system in front of any of us, we are pretty much guessing, er, I mean hypothesizing!