The boutiques inside department stores are still owned by the company of the boutique but ran by the department store. It's just a way for certain designers allow their items be sold in department stores and not lose that prestige. Theres more into it but that is mainly the reason I believe it is done.
Not only that, but alot of cities have $$$ and money, but just wouldn't make sense to have an actual flagship store.
Take for example Birmingham, Alabama or Austin, Texas. Size alone, those cities are huge, so it would make sense to have a Neiman Marcus or a Saks toaccommodate the clientele, rather than a Gucci Store, a LV store, etc.