IMO, I do like your idea having them to the sides. Aside from the point about avoiding restriction from the overflow box being in the way, and, you could create circular water motion. One end pointing parrallel to the water surface and the other end going further down the tank pointing at a 45*. Of water flow, but also depends of you stock likes it.
One downside is the plumbing will be exposed on the ends rather than the covered back - or do I have the wrong picture in my mind? What does the builder recommend? BTW, you dont really need a 90* if on the back. The loclines could handle the turn. Unless you're talking about the 90 from the back to the bulkhead ?