There's a file that doesn't get updated when you're upgrading from 1.2 to 1.3 instead of installing 1.3 fresh.
The file steam\steamapps\<user>\dystopia\Dystopia\cfg\user_default.scr defines what's in the "advanced" options menu, so some important options don't show up when you upgrade from 1.2. If you delete this file and then re-run dystopia it will create the new version
If you installed Dystopia 1.3 from scratch, instead of on top of a previous install, you don't have anything to worry about.
The specific things that this will fix are:
*the option to toggle between red/blue and red/green IFF will work
*there's an option to turn off the map paths
*there's an option to turn off the screen effect when you spawn
*there's an option to turn off that huge red X on your teammates