Wouldn't that mean that the nacelles would be facing backwards? I prefer the idea that it was still the front of the ship but the bridge was elsewhere. No need to always put it in the front, after all.I was always under the impression that the science vessel was supposed to be scaled up in relation to the scout ship. The script for the episode even noted that the ship was "half the size of the Enterprise-D." Also, I always assumed that the squared off section that used to be the scout ship cockpit was actually the engine room (and hence, the rear of the ship), since that's where the warp core was ejected from.
