Well, the MLS package is also the only way to see your local team, so they've got a bigger hammer there (even if you can also get it for free as a season ticket holder). If I had to buy Sunday Ticket, living in Philadelphia, to see the Eagles, that would be a very different situation.
tbh since I'm not strictly speaking a Union fan but am also not that interested in sticking with the Timbers (especially with most of their games starting at 10:30pm) I'm not sure I'm up for that extra $12.99 a month ($14.99 without existing + subscription). I'd certainly pay that to see the Eagles, but not necessarily for Sunday Ticket per se. It is very rare that my interest in other, non-Eagles NFL games isn't met by the national broadcasts.
It seems like it's not that different from what Comcast has always done - Apple wants overall subscribers and to sell hardware more than they need to make money selling the product, and they'll also get quite a bit of advertisting/sponsorship revenue that MLS probably won't.