Yeah, I think Roddenberry’s initial vision, the nacelles were set apart from the living areas because constant close contact with the source of the warp field was hazardous (and who knows, in time the Alcubierre drive may prove him right).
I think over time there’s just been this implication that the risk was reduced/eliminated thanks to advances in technology (spurred mostly by the narrative), and they stuck with the look basically out of Aesthetic^TM^.