[dogscoff]

The ONLY difference is that the neutral races are restricted to their homesystems- it is hard-coded that they cannot use warp points. There are a few unusual circumstances (which may or may not have been patched out in recent Versions of Gold) where they will use warp points, but by and large they just sit in one system and wait for you to conquer them.

You will also find that neutral races in vanilla se4 never use racial techs, but I think this is an AI restriction rather than a hard-coded one: That is, if you wanted to mod them to use racial techs, I believe you could.