...On Windows, for example, the board doesn't reset when you connect to it over USB.
hah !
maybe I had the wrong kind of board, but mine would reset every single time I opened a serial connection to it. be it using the world famous 'hyperterm' or any other windoze software we use in the lab.
and talking about complexity, there's already a jumper on the pcb and I easily managed not to misconfigure that, never touched it actually 
now to the topic of 'production'. this box I built is one of a kind. there won't be a 2nd one and we needed it asap and with usb, that's why I chose to take the whole arduino board as is and just add the missing parts on a bigger hole matrix board around it. no time to have a custom pcb built for it. and for people who might have to repair it some day it's way easier to find a complete µC board that is so nicely supported by this community.
finally I feel the need to say that thanks to the GREAT webpage and IDE, I managed to build this device (hardware + coding + waiting for parts) within just 1 1/2 weeks staring from zero.