Can you, dear reader, suggest how to get Arduino Unos fabricated in bulk with alternate header styles? I know SparkFun sells the Arduino Pro without headers, but I want something with downward facing male pins, or female headers with extended pins so that I can mount the board upright on a 'motherboard.' This is for embedment in a consumer product, so volume could be 500-2000 per year.
Have you contacted the Arduino folks?
Adjust the design for your actual needs. Do you need all the stuff that's actually on an Uno? Probably not if it is plugging into a motherboard.
For example, the reset switch, voltage regulator if 5V is available, the 3.3V regulator if you don't need to output that, perhaps the LEDs.
Maybe you want a crstal instead of a resonator. USB interface needed? Or will the motherboard take care of that? Want a uC with 2 serial ports and more memory?
www.cbas-usa.com in California can make all you need once you have a design.
I think they do turnkey as well. Or you have Digikey and your PCB supplier drop-shop parts right to cbas-usa.
If you want all IO pins on one edge, I have designed a card like that as well.
Surface mount or DIP processor?