Yeah, definitely overanalyzing this. Let her ride the bike and let her tell you what she needs. You're right that bikes are made for the "typical" male and so often don't fit a woman right without some tweaking. Offset on the seatpost is not the only way to deal with this issue; a saddle with longer rails will also give you greater adjustability. Lack of set back is not a super hard issue to deal with and you might want to talk to the LBS about a different saddle.
But, you are being rough on the LBS as well. You just bought a nice bike from him and then wrote:
"The guy (who actually seemed pretty nice and knowledgeable) told me that I am trying to be a perfectionist, and I need to let her enjoy the bike the way it is now. According to him proper knee position only matters that much in road biking world.
I think he is full of crap, because if she decides to get clipless shoes later, she will be screwed."
In my experience, bike guys who are "nice and knowledgeable" are not "full of crap" but are actually trying to be helpful. If you approach the guy with that kind of attitude, you'll have a tough time with him. There comes a point where any good will that is lost by pissing off a customer just isn't that big a deal because nothing you do will please the customer. Just my 2 cents worth.