Ted, I did not trust the factory settings without verification of some sort especially something so large that has travelled so far. When I set-up my MFT/3, the first thing I did was check all of the hardware securing the legs and the table board for proper torque. There is no specified torque per se, so I used discretion.
After snugging up a few loose bolts I went on with alignment of the fence. I used the clamping elements to square the miter fence to the table holes. After squaring the fence to the holes I made sure the gauge pointed dead-on at zero, tightened up all of the miter gauge hardware then installed the miter fence pinch brace.
Unlike Per's experience, my rail height adjuster stops were not accurately placed. The manual gives you some goofy something and 2/3 of an inch location on one side. With the miter fence set, I measured off the side with the more coherent specification and adjusted it as needed. I used a known good framing square to set the saw rail 90 degrees to the fence. My two saw rail height adjuster clamps did not snug down very well at all either. A little turn of the screws and they were much better.
With the saw rail now square to the fence and the height adjusters secured, I moved that little stop in the side rail up against it and locked it down. After carefully rechecking all hardware for tightness and again the miter fence and rail to be perfectly square, I sawed my 3mm deep relief groove into the table.
You can watch this video for more info on MFT/3 set-up too.