Well, I normally allow the LNAV to follow the route (lat and long) and check that my pos as plotted on a chart lies on that route. It matters not to me or my a/c whether it flies mag./true or grid, as long as it stays on the line, surely? I do not sit there working out variation every 10 mins. to make sure it is steering the correct mag heading +/- 5 degrees.
My 'route', both PLOG and FMC, is built on rhumb lines between waypoints, my PLOG shows true and mag tracks. The differences in variation data bases are pretty well irrelevant since the a/c will track the lat and long of the route regardless of variation, and even if it had NO variation db it would stay on track, wouldn't it?
Now, if I lose ALL my nav kit and have to DR across the area, apart from my being just a bit screwed, THAT is different and then variation becomes a significant factor.