I just remembered that I once posted about my test with the Mini Pro tram, and back then I got 0.004" front to back. But that was measured on an aluminium bed, not MDF, and as @mhotchin noted, MDF does its own thing sometimes. Something you can do is use a piece of glass on the wasteboard, and re-measure, see if the value is still the same?
Anyway I wouldn’t obsess about the value if you get nice clean surfaces at the bottom of milled pockets.