On string spacing
The R3 is close to he same string spacing the same as a R2 but it actually is a little bit wider string spacing, Tom is right, the R3 was actually designed for guitar with binding that are 1.680 (1 11/16")
The R2 is a 1.62 width, Tom and I use a 1.65 nut width since I personally dont like supper narrow nuts on guitars, we split the difference on the Modern by making it 1.64 Nut width.
As far as the over hang, it means nothing, the nut is secure and the original installations by Floyd had the nuts hanging over.
The Floyd nut was that width to securely clamps the strings, he never meant people to redesign the classic headstocks.
Here is the problem though, if you design a neck for a Floyd specifically you can not use the same design headstock for a non Floyd, On a Headstock adjustment you would need a deeper length adjuster nut or more the truss rod.
You would also need to either move the gears further away from the headstock or change the radius that goes to the headstock whihc would weaken the headstock. If you were then to use this same headstock geometry on a non Floyd guitar the strings would hit the wood behind the nut.
There is no win here and really nothing to fix.