Yes, that is how I've done it - patched the header file to modify CONFIG_EXTRA_ENV_SETTINGS.
The trouble is that, with MfgTool, it seems that a default (shipped with the tool) environment is programmed into the board. I can give it a custom .env [text] file to append/modify this default, so was wondering if there was anything in u-boot/yocto that already automatically generated this - or even something close to it - from my u-boot (i.e. whatever is in the source).
The header file itself contains other #defines in CONFIG_EXTRA_ENV_SETTINGS - perhaps a little more processing of it is needed. Or - more complex - parsing elf-style header info in the binary in order to find the region of the image with the env data?