Is it actually just the ILS that is misplaced? Most ILS approaches have a number of waypoints on the final approach path too. Has anyone checked whether these are lined up correctly with the ILS signal, or with the physical runway centreline?
Fixings these issues could well involve a lot more than just a simple ILS shift. All the corresponding approach waypoints may need adjusting too. And what about other approaches, they may be ever so slightly out of alignment too, only less noticeable.
My guess is the scenery itself is slightly misplaced. MSFS is the first version that uses satellite/aerial imagery as the basis for airport scenery creation. Maybe this produces slight position errors.
The navdata however, comes from an accurate database, much like it has for every other MS/P3D/XP simulator without issue, and is therefore probably correctly positioned.