- 1284P-PU, 1284P-AU, 1284P-MU all have the same device signature.
- That's one way to do it. I use my MKii to burn a bootloader to set the fuses, and then File:Upload using Programmer to load the sketch. Mostly because I don't like waiting around for Atmel Studio start up.
- Pins_arduino.h is the same for package to package. It maps the software names to port names. The software doesn't care how you then get from the port to the physical pin or what the physical pin numbers are.