Here's a photo of my mk3, size 600, the largest they make.
With the brakes I have fitted, the outside of the rack boss is obscured, but I have had a rack on the bike when I did lejog a few years ago, but that was an older Blackburn Expedition rack with the flat stays with the twist towards the end, and it was just possible to fit the rack ok on the outside of the boss without affecting the brake.
It does seem strange to design the boss location as it is, but maybe there's a reason for it.
In any case fitting the stays to the inside faces of the bosses is a perfectly adequate solution to the issue, i would use the long bolt from the outside with a nyloc nut to hold the stays method.