How about the fact that 2CP unlock is more fitting for an ability that has sort of limited use while Singe Stuka can attack anything and thus 3CP are more fitting to its potential?
Stuka raid usually destroys like one emplacement or two, but people usually don't cluster many emplacements close to one another because it is easy target for arty and, well, Stuka raid, also you cannot choose which side they come in, so they can be easier to shoot down by AA. Single Stuka can be sent in specific direction (to avoid AA) and you can sent it to any unit you want.
So your argument is "it makes more sense from "common sense" point of view" (which means pretty much "I feel it would be better"). My argument is "it makes more sense from gameplay point of view". I would say my argument is stronger