[Daynarr]

The game will use the default AI scripts nested in SE4\AI folder. Also there are 3 different default AI scripts there (Defensive, neutral and aggressive). You can change them when you create those emp files (Use minister style option). Also, when you make those files and you have script for that empire select 'Use race minister style' option. Now AI will use those scripts.
As for random selecting empires, the computer can random select only those empires that have their pictures located in \pictures\races folder. So, if you make custom empire that uses Cue Cappa pictures, only Cue Cappa can be selected.
It is not possible to have two same empires randomly selected.
If you use this Cue Cappa custom empire, Cue Cappa cannot be randomly selected.
You can add them using emp files as existing empire, though.