Only if you have dynamic rep on will they be linked, so if you leave that plug-in off, pick on whoever you like. Just don't make everyone angry at you.
Nice, yeah and there's a couple sectors down south of Terran space that are ripe for pirating. Vow of Allegiance I believe it is. There are some juicy targets that the Terrans fly, and some nice combat ships you could obtain from them as well, let alone the weapon systems. I hadn't thought of a play through like that, and I dislike the Paranid and Terrans alike, so I might just take both of them on (unless Paranid rep is linked with Teladi).
spoiler: Yes, it's called Tortuga, and it's home to the Yaki's home shipyard. It can be found through a jumpgate just off the north end of Armstrong's map when zoomed out. M5 pings will help to find it.