Changing MagVar should not cause any problems. The real issue comes in trying to move them. You are right that Addon Scenery Takes precedence over stock in most cases. However there is generally an 'exclusion' in the addon scenery file telling FS to not use the default. No such thing seems to be available for navaids/waypoints (other than terminal). So we get erratic results. Our research (done by Jim Vile) indicates that you can usually move such things a few miles without a problem. After that you will get duplication and two of the same navaid - not desirable. Worse you may cause a CTD if there is a route associated with the navaid (there will be a waypoint co-located with the navaid). Finally the safe move distance is not consistent and in the end became so small we just don't think it safe to move them at all...
That is not to say that things will work in some circumstances so you or others will certainly be able to show cases that disprove the above but generally it is a dangerous thing to do.
Even Changing "Magnetic Variation:, is opeing up Pandora's Box.
You will find that many CURRENT "REAL WORLD" Charts are still using really OLD values of Magnetic Variation.
For Example KOSH OSHKOSH
REAL WORD CHARTS: Magnetic Variation from 1975 is 1° East
Chart shows ILS 36 heading to be 359 degrees. ( based on that 1975 Variation)
But Today, when you fly the ILS, you will be on a Magnetic Heading of about 4.5 degrees, because the Magnetic variation has changed significantly from 1975 ( Big Surprise)
But in FSX, MS took current Magnetic Variations at the time of FS8 / FSX, so in FSX, the magnetic Variation is BOTH, not the same as Current Real World Charts, and also not the same as the current REAL World variations.
So, what are you intending to set the Variation to ? Chart, FSX or Current 2011 Real world.
Yes, in case you are wondering, OSHKOSH's Approach Plates are way due for a Real World Update to the correct Magnetic Variation. Current Chart value is now more than 5 degrees in error !!! (Your tax dollar NOT at work ? )
Interesting stuff !!
Geoff