Join Date: Jan 2012
Location: Not every shadow, but any shadow
My take is that the Unexpected Problems only apply to the base of the charger being obstructed by the base of another unit, or tree or whatever.
All of the charge rules talk about base to base contact and there isn't any clear indication that I can see of what to do about parts of the model obstructing things.
Given the nature of flyers to be at differing altitudes and that it is generally only those on flying bases that actually overhang the base I'd say that taking them off the base to fit in is the way to go.