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That's what NMEA-0183 (and latterly, NMEA-2000) is supposed to cover: these devices can talk to each other.
Although why an autopilot needs to "talk" to more than a fluxgate compass is beyond me, as I believe linking a pilot to a chartplotter and a bunch of GPS waypoints is risky business indeed (see my post in the "Obsolete Sextant" thread.
GPS can be disrupted, and while I suppose you could sail over a giant dump of lodestone, generally, magnetic forces of the Earth are relatively stable and predictable. That may change, but I doubt you and I will be sailing still!