I figured out what I was doing wrong, and wanted to post the resolution in case anyone else encounters the same issue.

There are two types of settings on the server, those that cannot be changed "live" (like Flare Stack burn rate) and those that can (like LTN notification settings). For the ones ...

I've got a headless server with a few mods. I want to change the default value for a few settings on a few mods but for the life of me I can't get it working.

Here's what I'm doing:

1) Open up Factorio
2) From main menu, go to settings --> mod settings
3) Adjust settings for Flare Stack and LTN
4 ...