Yep. See Proportions mod, for example.
However, I think there is an abstract rationale that can be applied to make sense of the basic set. That is, engines can be thought of as _producing_ energy as they burn fuel. As such, they are a power source. Or, the engines can be seen to reduce the ship class' ability to include other components by 10kT, but in actuality they themselves are still larger than the supply storage units - it's just that increasing engines doesn't reduce the size class' potential as much. Also, there is the game balance rationale that extending operating range should be somewhat expensive. All told though, I agree with you, hence my mod.
PvK