The booking goes exactly as described. The "linking" of reservations is minimal: I think it's effectively just a note in the record. But it means that when I call in (eg in IRROPS) the agent immediately sees the other record and can work on them both easily. Also, when you view the reservation on alaskaair.com, there's a direct link to the linked record(s) so you don't have to lookup the other confirmation code. I don't believe automated rebooking tools connect the records. I don't recall having trouble because of that, though I don't remember if I've had IRROPS when traveling on a companion fare (or other ticket) booked like this.