You will always see a run out across the x axis. Especially if you have the dial indicator mounted to the front of the extruder assembly. The x rods flex. The x axis rails need to be a larger diameter or supported or just replaced with a profiled rail to eliminate the flex. This irritated me early on as well but after several posts and comments from others here as well as the Lulzbot folks, I realized it doesn’t really affect the print.
After you have your bed leveled using the bed leveling g-code, move the extruder to the center of the bed and set your home gap to 0.005". Then, set up a smaller part to print in the center of the bed. Then, print the same part at the left or right side of the bed. You will probably find that it does ok even though there is a variance in the extruder tip to bed gap between those two build locations.