Having delivered a few yachts that had the autopilot interfaced with a desired chartplotter
waypoints is that the REAL problem is that in order to make the system work
input is required to "tell" the system just where you are thought to be. The usual systems only have a response time of a second (at best) or worst, especially if your chart "plotter" info is delivered from a windows based laptop
Even with a reliable chart plotter (translation: no windows based system involved) the apparent response time of the autopilot to the "system" becomes encumbered and, therefore, seems to be sluggish or downright wrong. If you are in heavy seas you will need to defeat such inputs to the autopilot and just give it the desired heading, piecemeal if you will, without a GPS
input and you will have much better chance of not falling off course causing a broach going downwind or downseas. Sorry, yet that is the state of things as they are now.