Wind resistance is the primary force slowing you down at speeds where riders care about such things. The tiny micro-accelerations after every dead zone add up in spent calories when you have a more massive bike+rider system.
That's my point exactly, wind resistance is the principal loss of energy.
The microaccelerations in the dead zone will be lesser in magnitude when you have a heavier bike plus system, but it will be more calories per m/s to recoup - while a lighter system will accelerate easier but have more acceleration to do. In the end the dead zone acceleration are calorically going to be exactly the same no matter the weight.