Some anwers on your questions:
1. The Atmolight for 1 thing can support 4 sides and even more (Momolight is limmited to 3 led lights (top, left and right). Next to that the software looks much more tunable then the Momolight. But I must say, new software is being developed for the Momolight, for example, last month a newer version came available which made it possible to have also moodlight with momolight. With moodlight you can upload you own 'light-show' and play it without having to turn on your computer.
2. The first design of Atmolight was not for Windows, but nowadays they also have software which supports windows fully.
3. I ordered 10 PCB's (need to do some experimenting

). Basically minimum order amounts is only 1 PCB, but there are setup costs involved. For the 10 PCB's I paid in total 42 euro, including shipment, of which 20 euro was for starting costs. The more PCB's I order, the less they cost per piece.
The main costs for building a system like Atmolight or Momolight are not in the PCB's or components for the PCB's, they are in the LED stripes.
About the A-R-E system: In principle it can support up to 4 channels (top/bottom/left/right), but I must say it is a pretty expensive system, paying rougly 50 to 60 euro per extra LED bar!!! Still it is a system with an enermous amount of options.