Re: Don't quote me
It depends. Later versions of warp technology possibly allow the warp field to be manipulated without risk to the crew. There are warp capable shuttles by the time Picard was commanding the Enterprise D, so I guess they got the kinks ironed out.
Perhaps bigger warp fields are harder to manage safely so the nacelles have to be set away from the ship? This would make a kind of fictional-universe sense as it's usually the bigger ships that have nacelles set away from the main hull. Defiant is pretty small compared to a Galaxy class.
(I'm trying to think of a federation ship that breaks this 'rule'. The Nebula class possibly, it has a Galaxy class size saucer section with a Miranda style nacelle layout.)
Probably thinking too hard about this now.