is there a way to...

[Narrew]

over-ride the treaty settings. Lets say I am a xenophobic race, and I am willing to have a treaty with someone, as long as they do not go through a Warp point, can I set ships/mine/sat fields on auto attack anything that enters that sector?

[narf poit chez BOOM]

nope. sign a treaty and you'll have ai ships wandering with impunity through your secter's. just like civ. except in civ, you can tell them to remove there units. and, no matter how many times THEY'VE told you to remove your units, when you dare tell them that, they'll get mad at you and soon your at war.

[Ed Kolis]

No, once you have a treaty of Non-Aggression or higher, the other empire's ships can freely pass through your space.

So take advantage of it - lay mines on his critical warp points in case he ever gets ungrateful and decides to break the treaty!