Of all the engine components, the main reactor would need to be the most accessible if something went wonky. How'd you
like to be the poor shlub who has to crawl all the way up those damn pylons to cut off the power flow or the ship is gonna blow up in five minutes....and it takes twenty minutes to crawl up that pylon? And maybe have to do the same thing with the other pylon? As opposed to twenty seconds to get to the other side of the engine room and throw a couple of switches?
The truth of the matter is that they probaby didn't think through that aspect of the ship's power setup completely (hence, the contradictory references from episode to episode, sometimes from scene to scene), but in keeping with Jefferies' stated philosophy of keeping the stuff you need to get at in as accessible a position as possible, you'd definitely NOT
want your main power source in the most inaccessible part of the ship, you'd want it where you can get at it as fast as freaking possible. You also don't want your main power source in a location that's just begging to be shot off by some smartass Klingon who's a really good marksman with a disruptor cannon.
As for the nacelles, it's not the power
that makes them so dangerous, it's what they do
with that power that requires them to be held out away from the main hull. In function, a M/AMRC is simpler than a fusion reactor, i.e., instead of having to induce a fusion reactor on some poor unsuspecting hydrogen atoms, which is pretty power intensive to begin with, with a matter/antimatter reaction, you just feed in protons and antiprotons from either end and they pretty much do the power generation all on their own, with the big trick being the containment part and channeling all that high energy plasma to the warp engines and wherever else it's needed.