Yeah, PvK's observation is good. An engine is probably something mounted in a 'nacelle' sticking out of the ship rather than actually embedded in the hull. So, it's not necessarily illogical that they don't match other components 1-to-1 in space usage or supply storage. 
Hmm, I still wish we had something like 'battle pods' though.  

  I tried creating a component with negative size and the game won't load the data file...