I am a bit confused. As far as I recall, most of the serious mobs are tied to a DinkleBot-Lock(TM) and you cant progress as long as anything is left to bite him in his shiny metal ass.
So I dont see how it is possible to skip anything but trash mobs?
And regardless, in the context of the game, strikes are commando raids to take out a high value target, not a major offensive to wipe out the enemy.
The mathematical part seems logical on the surface, [i]if[/i] you are going for loot per strike. But in reality the unit is loot per hour.
So I am betting my own rewards on there being more loot in doing 4 fast strikes in an hour than doing 2 slow strikes in the same amount of time. I wouldn't be surprised if you kill more high level mobs too, since you will be killing twice as many waves.