Pretty sure setting <iAppearance>-1</iAppearance> (in the feature xml) will stop those features from being placed on map by all map scripts.
All the scripts use this condition for placing random feature at a plot.
if random() * 10000 < GC.getFeatureInfo(iI).getAppearanceProbability():
We don't need a new tag.
Edit: Well, it helped, now those beacon reefs are only placed within fat cross of players starting positions, so appearance probability is ignored in the dll code that spruce up the yields surrounding the starting position for all players. That's easy to fix though.