Origin have their own questline, even some questline with which they will get in each other way, I think, because they sometimes need the same people for different reasons. In some talks you will have option who are only from this character and therefore tagged with their name. Of course you could follow the quest even if they are only companions, but I think as main characters it works smoother.
Also the source skills from origins are more unique than the skill from customs, but on the other hand you can't change their name. ^^