Ian,
In the case that you have mentioned... It makes perfect sense...

EFI stores a certificate that authenticates the MS cert, and unlocks the partition that holds your windows installation. This would not prevent the booting of a secondary operating system, but could potentially prevent moving data between a 3rd party OS and your Windows installation.

This would prevent the biggest issue with disk security today, the use of 3rd party boot disks that allow you to access the local disk, crack a local password, plant a Trojan, and then return the computer to an unsuspecting victim... Who then boots up the computer, uses their domain password, thus exposing their data and credentials...
But the decision to go with EFI could also be beneficial to booting other OS as well, if Linux and other 3rd parties took advantage of the same features, you wouldn't have the age old issues of fighting between multiple boot managers.