[" what if the Terran player could have the Argon, Split, Boron, Paranid and yeah the Teladi too arrested by a-lerting some NPC that a commonwealth race member is on a Terran station and have it linked to notoriety changes "]
Missions offers from NPC not related (and even enemies) to the sector/station owners is by design since X3TC, Terran are no exception.
Relation impact will only affect the factions involved in the mission. Obviously any interactions in space will have the standard effects with the owners of said space, its only indirectly linked to the missions though.
I look at it this way - races still travel freely throughout the universe. Many of those NPCs, while of a race and giving a race reward, could still be travelers and merchants, etc. Think of yourself, no matter what race you are, you aren't instantly hunted and killed by most ships of races you are allied with. You can be an argon and friendly with terrans, for example.