The Musician's Friend website lists a price range of MSRP ($1046-$1092), not the same as on PRS site, where it lists them @ $1092 w/cordura gig bag). They also list some guitars "w/bag", and others w/o that annotation.
It's plain as day what you're getting and the price you're paying. Either buy it at that price (w/o the gig bag) or don't. PRS has accommodated their dealers (in this case Musician's Friend/Guitar Center) but selling some of the guitars to them w/o gig bags. That is what they want. The dealer then sells them with or w/o the bags.
The customer decides to make the purchase or not.
Why is this an issue?