ID:1714338
 
(See the best response by Jaysburn.)
Is it possible to have an atom that isn't visible to the player with an overlay that is visible?

By "isn't visible" I mean is obstructed from view due to an opaque object.
Best response
Everything on the map blocked by opaque objects is hidden from view, so not really. The only things that can show up over opacity are screen objects, so you'd have to do it through them I believe. Possible, but tricky.
They should add something so that you can override opaque and put like custom overlays and crap.