Pete, my EBMM EVH nut sits exactly like that (overhang), but it's a 1 5/8 neck, so there's no gap on the sides. Oh, and I have 3 shims under the nut!!
I think somebody hit the nail on the head in terms of them just choosing not to redesign the neck to accomodate the floyd nut. That would be my guess. I can sort of understand that, especially since I'm not convinced the overhang would make any difference in terms of tone or performance.
As for the shim, if none of the Charvels are shimmed, is it because they don't need them or because the QC on the way out the door isn't tight enough to really care? The presence of the shim on the Anderson, to me, says that somebody went the extra step to get the setup as perfect as possible. Think of the floyd nut as a precut, preslotted plastic nut blank you'd get from MF. Would you trust a factory that slapped the precut, preslotted nut on every neck and sent it out the door? Sure you get lucky sometimes and the fit is great right out of the gate, but if the Floyd nut is a hair too low, you either live with it, shim it, or cut a new neck. Shimming it seems the right choice to me.
I just have a hard time buying the "lack of attention to detail" argument that some have posted. Guys like Anderson, Suhr, etc. - I would bet the details pretty much consume their lives...
I will say though that the gap on the sides would probably bug the shit out of me. Especially considering that if somebody is looking for a 1 11/16th floyded guitar, they might be expecting that string spacing at the nut and a 1 5/8th nut might not be an improvement to them...but it's obviously a conscious choice he made.