It's just a shortcut aid based on the OEM's ergonomics engineering. The sweet spot is considered to be with your eyes high enough to see down to the base of the windshield without obstructing anything on the instrument panel.
This puts your preferred sight line roughly on the plane of the coaming/glareshield extending toward you from the base of the windshield (or slightly above or below), when the seat is positioned to the typical for/aft position for a comfortable hold on the control wheel (roughly a forearm's length from your torso).
When you get in there are 3 steps:
- Set the seat for and aft to suit your forearm length to the control wheel or side stick.
- Set the seat height to align the balls, or whatever your personal preference is.
- Set the rudder pedal adjustment (called the stature adjustment) to your leg length, making sure you can apply full rudder plus push the brake on that side fully on with your toe while your leg is stretched out.
Not everybody likes the recommended location set by the balls. When I was flying CRJs, which had the balls on the center post, I would ignore them most of the time and just set the height to put my sight line where I could just see the top surface of the glareshield, which, as it happens, more or less aligns the balls.
The eye height most pilots will set with or without the balls tends to be the same, and the seat setting you find when you get in tends to reflect the torso length of the previous pilot. I have a long torso and short legs, kind of orangutan-ish, so the next person after me usually would find the seat set pretty close to the floor.