boards
I really have absolutely zero experience with designing commercial solutions using Arduinos, but I would assume that a standard approach would be to use an off-the-shelf arduino-compatible board to prototype, then just embed an appropriate atmega chip and resonator onto the final product.
Given that many industrial applications are cost-sensitive to the point that a few extra resistors makes a big difference, why would you ever embed a "real" arduino in a commercial product - considering it probably costs at least $20 more than just embedding the bare minimum components?
Taking it a step further, wouldn't it also likely be a standard approach to just burn the finished program to a blank chip, rather than using a chip with a bootloader on it?
Then again I suppose it's all fairly application-specific.