The FMC only reads the data from the Prepar3D\Captain_Sim\navigation folder (when you program the route/flight plan in the FMC). All waypoints and fixes are listed in there. Depending on when the fixes and waypoints in P3D were done (if they are the same as FSX, then that was 2006 or somewhere around then), whereas the navigation data that comes with the 757 v4.6 is dated 07/APR/2011 - 04/MAY/2011 (AIRAC 1104), so the actual locations of the some fixes/waypoint will be different from what P3D has.

If you want to uses the default fixes/waypoints/jetways of P3D, then you create the route using the P3D flight planer, save it and load it with the FMC. You will still need to add a SID and a STAR if you do that. So what happens is the coordinates for the fixes and waypoints are provided by the flight plan itself (the FMC is reading the flight plan data), and not from the data in the Prepar3D\Captain_Sim\navigation folder. The SID and STAR data will be added to the FMC flight plan, based on the coordinates in the Prepar3D\Captain_Sim\navigation sids.db and star.db files.

This applies to Prepar3D v2 as well, if that's what you are using. ;)