Are you referring to the fact that the expansion specific files are stored in the AI War/Expansions/1/ folder? If this is the case then this is internal, logical file structure for the game files that most players will never need to even look at. If your plan is to modify certain files such as images to customize your gameplay experience, this is perfectly acceptable but not something that is officially supported by Arcen Games.
Of course, if the TZR expansion is referred to as 'expansion 1' somewhere within the game in such a way that players might be confused, please let us know precisely where this can be found.