Unless your console has sold as well as the PS2 did, almost all exclusivity deals come at a price ...
Microsoft probably offered Square enough money to make Square-Enix to consider going multiplatform, SquareEnix went to Sony to see if they would match the offer to stay exclusive, they may have traded offers for some time before Microsoft was willing to spend more to make the game multiplatform than Sony was to keep it exclusive. The fact that Microsoft probably generates a decent profit off of each console after you consider all revenue gives them the option to start using their financial resources to attract third party development ...
Believe it or not, this is why losing money on hardware doesn't make sense and doesn't add value to the consumer. While Sony fans may receive $100 in "Free Technology" Microsoft fans will now gain access to games that they wouldn't have if Microsoft's gaming division wasn't profitable.
