But you bring up a really good point, which is that the borders of this game aren't political borders in the same sense as most 4x games. They grand you no rights to the territory. Others can freely pass through, settle and build there. They really represent the area where your culture is dominant, your only real control is over the planets you settle and the star bases you build.
They are treated as political borders now, apparently. Trespassing in foreign territory causes diplomatic penalties, according to what Mormegil said here. Also, there are Open/Close Border treaties in the files.
Really makes me wonder how certain cases will be treated. Like, for example, you have colonised some planets, and they get enveloped by foreign influence later. Will the other race now get pissed at you for "trespassing"?