Bringing the warpcore all the way back to the section between the pontoons (spelling??) seems like a bad idea. Like to you said, easy target. But also difficult to reach for maintanance and such. For somebody who used to work with cars a little bit, I can tell you, you want the engine to have easy acces. The way it was done in ENT makes sense. Sure, it can seem dangerous. But nuclear subs have their powercores in the ship, right? Not dangling out back.
As for the transporter.... I say keep it, but use it like it was supposed to. Approved for bio-matter, but people being dead scared of it. They got used to it way to fast IMO.