My friend who works in the industry had a couple of theories about this.
It has to do with union/nonunion workers, the cost of renting the venue, and all the other expenses that have to do with MSG. When QPR played the two one-off gigs, they did Continental Airlines because it's nonunion, and it's otherwise much cheaper to play there instead of MSG.
I think you're seeing a pattern in some of the dates they've booked all over the country--Worcester instead of Boston, for example--in which they're doing the same thing. In many ways, it's genius; in other ways, they're not playing some of the big-time marquee joints.
I would have loved to see them play the Garden, but like you said about Billy Joel, he's a hometown artist. If the situations were reversed in, say, London, I'd say the situation would change. That said, Wembley Pavillion sucked.