And if you're in the camp where the TOS warp nacelles held the warp engines, then the engineering hull was the place where all the energy from those nacelles was shunted for ship wide use. And in the case of ejection, it was the nacelles being popped off... I posted a thread a while ago where I went through the 79 episodes of dialogue using key word searches, and that justified them being the "power pods" as was also labelled on an early sketch of the Enterprise.
Anyway- not the point completely, but there is no reason that every ship throughout the history of the Federation would contain the same type of warp engine.
Let's say something like the past 100 years of ships having similar characteristics like propellers, but to drive those propellers, we had (coal) steam, diesel electric, diesel, gas, nuclear (steam again), electric... et c... Regardless of the location of the power source, my point is that there were different sources throughout a short period of time. Having warp power coming from the Nacelles could have been revolutionary, but then deemed not needed on following classed due to different engine power source configurations... Whatever the reason... Work now!