Ok, now I know I'm not crazy. I've experienced this before when the cache-prototype-data option was included. It wasn't in my config.ini for quite some time. Now I can reproduce it.
New options do NOT appear in the config.ini until a setting has been changed, within the Factorio GUI, and "confirm" is clicked. You can't just click on confirm because if nothing changed, it doesn't write to config.ini. That triggers a rewrite of the config.ini, and then POOF, new options appear. That, or delete config.ini. Bug?