As for as a sanity check (hehe, as if you, of all people, need one of those), what is described in that write up seems quite workable. Other than the single image requirement for programming during manufacturing, I don't think I quite understood the need for single image requirement after initial programming -- not that it won't work, mind you, but with the PC and boot facilities for reprogramming, all the pieces seem to be in place without having to combine.

This does not usually apply, but I have sometimes included a means to reprogram the boot area from the application side, but that's only in applications where there might be a need the risk of doing so is acceptable.

Again, the way you're going about it looks hunky-dory. I've just always done 'em with separate boot and application images and for manufacturing, combined the HEX files by:

    sed -e '$d' boot.hex | cat - app.hex > mfg.hex

This deletes the last line of the boot HEX file (assumed to be the end-of-file record) and tacks on the application HEX file, writing the manufacturing HEX file.