In our case it is the end of physical travel for the hydraulic rams. In effect, the ram physically reaches the end of the cylinder - no matter how much more you try to drive it its not moving.
This causes big loads elsewhere in both the pump and electronics. The autopilot box detects this and reports it as a warning.
That roll pin is taking all the force the motor can produce at that point.
You should be able to set the max angle of the rudder so you don’t physically hit it. Whose autopilot do you have?
When we reset the autopilot after replacing the motor, we knocked a couple of degrees off, just as you suggested. My feeling is that each time we get “Rudder Limit reached” as a warning, it may strain the autopilot motor. We also align our rudders quick frequently, before any long passage.
We have Garmin electronics and Lacombe and Schmitt driver. I believe the Garmin device defaults to 10 degrees upon setup, which is fine. Garmin gives you ability to customize and change rudder gain as well.