If you turn your float glass or whatever you use about the spindle axis 180 degrees and then average the measurements that would account for any surface deviation in your reference surface – you could in theory use anything smooth – just use a marker pen in the spindle to mark the centre and the y axis to draw a line front to back and use these to aid accurate turning.
I dont recall what is or isn't acceptable by numbers, I always find fly cutting highlights what is unacceptable, if the lagging edge of the cutter leaves equally light ring marks cutting to the left, and to the right – that's spot on for me!
Front to back is a little trickier, but again if fly cutting cut down the center of the part, then when you unlock and move the Y to give a slight overlap (say 5mm) to cut the front and back the overlap should just lightly skim the initial center cut leaving rings but not really removing anything. I don't think you can adjust this anyway without rescraping the saddle, knee or column (or all 3!!) and determining which bit needs scraping and how much is a whole other game – although very rewarding (I thoroughly enjoy the meticulous metrology of it, each to their own!)