tnarg - as resident alien 2 explained, it boils down to what files each mod uses to implement the changes. This is somewhat tricky to determine, as some mods will include the entire SE4\Data directory in their mod, and you cannot really see whether or not they changed anything unless you compare file dates. The concept is explained in more detail in a two part article which begins here:
http://www.cgOnline.com/tips/spaceempir-04-t1.html
I know as far as our TDM-ModPack is concerned, we modify the "Formations.txt" file (we added a ton more formations) and make a slight tweak to the "Settings.txt" file (essentially increasing the default number of ships/units allowed). That is it. When combining with other mods (such as component or tech tree mods) in a lot of cases the AI will not use the new techs or components unless they are specifically modded for that data mod, so this will give the human players an unfair advantage.
Hope this helps
-TG