jtw11:
Alternatively, are you implying I can simply get rid of onboard USB to Serial conversion and use a cable like this, that connects to ICSP pins to program the chip from the Arduino IDE?
Yes, if your project does not need USB connectivity, you can upload your sketch using ICSP. You don't need a bootloader. This is what I always do when I migrate projects to dedicated hardware. Put a 6-pin ICSP header on your board. You need either an ISP (e.g. the AVRISP MkII), or you can configure an Arduino to be an ISP by uploading the ArduinoISP sketch to it.