It's not the placement of the warp core that's the topic. The warp nacelles have to be away from the ship itself because of the radiation, which on the defiant class the nacelles must have been heavily shielded. The warp core is in a centralized location that's close to the anti-deuterium pods and dueterium tank. You can't really put those into the nacelle pylons or the nacelles, there wouldn't be enough room. So they put the warp core (or in the Constitution class the reaction room, there wasn't a centralized warp core on that ship.) as close to the nacelles as possible. Also, the warp plasma gets accelerated VIA the warp conduits, so they have to be a certain length for this to happen. And warp core is simply a specific term for what the overal FTL engines do as a whole. The subspace fields warp the area of space around it to partially submerge it into subspace while still being active in our space. It can also be called "main reactor", and engineering can also be called "the reactor room". It's all synonyms.