I just reviewed the waypoints we entered from Sean and Heather's guidebooks onto the Navionics Caribbean & South America charting for our time in Mexico. I found no major discrepancies. The Navionics charting isn't perfect. For example, it showed us anchored on a nonexistent island in the bay near Candeleros Point on the inside of Baja (south of Danzante Island). One annoyance was what appeared to be nearly random sprinkling of rocks often in deep water along much of the coastline. Our other resources did not show these rocks, but we stayed clear anyway. We were a bit suspicious that they even existed. Perhaps they were deep and not a threat to shoal draft vessels.
One feature much needed is a rubber-banding ability to move intermediate waypoints along a route. The current version requires backing up from the later waypoints to change an earlier one. Then you have to add the later waypoints all over again.
So, the Navionics charting on the iPad was indispensible for us, but we always repeat at least once a day: "We are sailing in the real world, not a video game!!!"