You may still want to send the overkill as interception scrambles are becoming more and more common and so sending extra bombers to hit the bases (or just the factory) and also tacs and fighters is smart as free casualties, and overkill is a method of deterrence, not just damage-dealing.
The total power/money imbalance (Ger v USSR) of the Dark Skies is so great that guaranteeing the 20 damage on Moscow must be worth 1 bomber lost per run, because our house players consistently bomb Moscow into dust turn after turn losing 1 bomber on average per round (to AAA and interception).