The current nav is confusing because it uses two different sets of maps.
The navigation routing software (Navigon/Garmin) uses an offline map database stored onboard. This map data is supposed to be updated annually, though the current US maps appear to be about 2-3 years out-of-date. The routing software uses this to calculate the routes - and this is the map displayed on the S/X dashboard.
The center console display uses Google map/satellite data which is downloaded from Google's server (which is why the maps can be very slow to refresh at time - Tesla does not appear to be caching any of the Google maps onboard). Google is very good at detecting road changes, the map data appears to get updated within a day or two after a road has changed; the satellite map may take a little longer before it will show the updated roads.
The navigation route is layered ontop of the Google maps.
When the two maps don't match (which happens in areas where there has been construction in the last few years), the route will follow the older maps (even though those roads may not exist and completely ignoring roads added in the last year or two). You can see this issue when driving in an area with changed roads because the dashboard map won't look the same as the console/Google maps.
Hopefully with NAV 2.0, Tesla will get back to using a single map database for routing and for display - and eliminate this confusion...
As for the speed limit data - the TomTom database is a step backward. AP 2 relies on that data for automatically setting the cruising speed or restricting AutoSteer usage. For non-AP cars, it's a very good question - since the data is likely already in the car, why shouldn't the speed limit data also be used for non-AP cars???