I've never heard of the missile behaving differently when it uses waypoints, but I guess it is possible that it might behave differently if the right-click method does not actually set the waypoints automatically but actually hits the target building itself. (although if it did that, I would expect it wouldn't do splash damage like it normally does). I'd still try moving the target around to try to find someplace where the missile detonates instead of crashes.
As for the waypoint trigger, try actually selecting Type Civilian, Missile. Or even Civilian, missile, TLAM.
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