Man, 1/10th is not much. I am also surprised to see those photos since I just spec'd a VF-3YT for work (and now I'm rethinking it).
I'm sure the issue is due to rigidity. I can remember thinking when I bought my Acra knee-mill, I thought it was a massive piece of unbendable iron. Then, while playing with a height presetter, I discovered that I could turn the LED on and off with just finger pressure on the top of the casting. No matter how rigid we think these machines are, deflection in the tooling, the workholding and the casting are real.
At under 0.0005, I'd bet that it's nothing more than the mass of the machine changing directions, that is causing flex. I'd guess that Haas might need to work on their acceleration/deceleration parameters to reduce that, in the YT machines.