There are no alliances that the game enforces. Human players may chose to work together and the AI may chose to ignore a certain player, though.
Type "dom3 --help" on the command line and you will see the whole configuration options for the dedicated server. Comparing these options with the GUI when creating a game helps to understand them, although some parameters strangely work differently from what you are doing in the GUI.
you can set the AI to be allied with eachother using map editor commands. I forget which ones, but there is a quick reference for map editor commands thread, maybe by gandalf. note: i have not tested this.