So that could actually be the texture of your table, paper, or too much pressure on the pen. I’m not convinced it’s the machine.
As for your other calibration. Each corner is at the same height and the diagonals are as close as you can get them? 1/8″ is kinda far off, but yeah parallelograms and ovals. But if it’s close enough for you don’t sweat it, Some people get a little carried away with those things.