Most of us are using galvanized steel conduit, it is much less circular than the stainless. Being .08mm off is very good your tubes which probably flex more than that over there span from there own weight. The bearing holders flex to compensate for unevenness.
If you want to replace the bearings with another type you will be making a whole new machine. You are now making modifications off your own assumptions of how you think my design will behave. I strongly urge you to try the machine before you redesign it. There are plenty of untested modifications already out there.
Tolerances are dependent on your design tolerances. Tons of people are cutting plywood I could only imagine that they would be very happy being within a 1/16″ over a few feet on a 4′ x 4′ machine. If you are making PCB’s your machine will be much smaller and your tolerance will be expected to be much higher. User dependent and a question I can not answer.
You should print out a piece and see if it meets your expectations, sounds like you might be expecting a little too much from a $500 cnc.
Please let me know how you feel about it if you decide to try it.