It's pretty similar to what I had in mind. I had to do it once before some years ago, and the company was a stickler for verbose documentation, so I have a well trodden path of my own to follow.

Regarding this:

I also am a firm believer in building the product code in a manner where the boot loader and the application part of the program are compiled and linked in a single build process. This makes it very easy to support and maintain factory programming images without extra steps to do double image programming.

You then have a build option to compile the application without the bootloader I assume? After version 1.00 rolls out the door you only want to update the app...