About the layout. There is the simple explanation and the complicated one.
Simple -Orion are early game and Atlantians later game. Players only have to really deal with one area of the 'frigate factory' for a good part of the game. Keeps things from being messing and having to jump back and forth constantly while building your early-mid game fleet. Sure, you have to hop to cruiser tab to get the starbase and anti-module, but you're also tempted with the Atlantian ships, so when you reach that magic point when you tech up for the Atlantian ships they are also all in one area.
Complex -two different races even though united. Orion are masters of cybermechanical technology. Atlantians are masters of biomechanical technology -even though their ships aren't living, sentient creatures. The technologies are so far apart that it'd be like having a Mercedes factory occasionally have to put out a tank and the tank factory having to churn out the occasional Mercedes. Very different stuff really, so best to have them separated into different areas.
But why the starbase constructor and antimodule in the Atlantian section??? We ran out of room on the other side. Sorry, but that's it really. If we'd started 7DS to be 100% 16:9 widescreen with minimum height resolution of 1024, lots of people would be left out -but we'd be able to totally scretch things out like you wouldn't believe. However, it's a hardcoded feature that you can't have more than 9 slots and then "Return" button.
We tried to preserve as much of the layout for Orion ships as possible. You've got some odd build values. Watch this on 720 and full screen. Most agreed it is just easier to deal with Orion in one area and Atlantians in the other. We aren't segregationists, it just worked easier.
Seeing the different values, I wondered if I screwed up something and left this in the developer 6m version.