No, it would not bother me to play in a campaign setting with which other players in the group were much more familiar. That said, the details given by the OP suggest to me that the problem she faces has more to do with general social dynamics than with gaming-specific concerns. Scarcely informed speculation and unsolicited advice follow.
Elf Witch, you are likely correct that your friend simply doesn't trust you and your roommate to run a game that fairly allows all the players to shine. For the sake of your friendship, I suggest that you don't take this lack of trust as a personal slight but as a symptom of a problem that you can help her to overcome. It sounds like she has had bad experiences in the past with being an outsider in her gaming group, in particular with the Shadowrun game you mentioned. Maybe she could have chosen a different character background, but maybe she simply didn't know that your group cared more about the integrity of the role-playing than the meta-game concern of building team cohesion among the players. Regardless, she had a bad experience; once bitten, twice shy.
The proposed Kalamar campaign no doubt gave your friend some qualms. She may fear being in another situation where she's not a member of the ingroup, and must wait for you and the DM to dole out knowledge that you two already share or to explain in jokes you have developed. The fact that you and the DM are roommates immediately creates an explicit ingroup that your friend simply cannot join. The fact that you developed your character so quickly confirmed her fears that you two are going to do your own thing, that you two will have several conversations about the game that naturally exclude her. No matter you intentions, living with the DM will probably give you many more opportunities to shape the campaign than your friend will have. Finally, the fact that your chosen character will be the face man and have all sorts or in-character knowledge about the world confirms that your character will probably call the shots for the group, and she'll just be along for the ride.
Or I could be completely wrong. However, if I have guessed more or less correctly, confronting your friend and forcing her to admit her lack of faith in the fairness of the proposed Kalamar game will only establish an adversarial relationship. Allow her to save face, and take steps to ensure that she feels fully included in the group, instead of a second-class citizen. (Important: I do not mean to suggest that you have treated her like one, but such treatment is evidently what she fears. And if our friends don't make allowances for our weaknesses, who will?)