Will it be a toggle for hd or will the ultra graphics be so superior that it would be overkill
Should we expect better than witcher 3 graphic quality with rocks, water, lighting etc or is the game more than likely to require several mods to get to that point

No idea what you're asking with that first bit.

I do expect it to be "better" graphics than Skyrim, since it isn't being developed for previous-gen consoles.

I don't expect it to look like Witcher 3 or Crysis.

toggle hd like what they did for halo anniversary?

Basically will it be hd right out of the box or even close to that quality

Will water, trees and other environmental effects be on par with w3 or will it be up to modding community to make it look as good

I understand we only have a small sample so far so its nore of a guess

Fallout 4 will look decent out of the box, but I'm sure somebody, or Bethesda, will release better textures at some point.

We have no idea about HD texture packs released by Bethesda quite yet. The only thing thats certain is that PC users are going to be able to render it at whatever high resolutions their monitor can support. Bethesda hasnt really pushed the graphics of their worlds since the Morrowind and Oblivion days, but then I could fill a entire thread with speculation as to why that is. What you see in the pre-release footage is going to be close to what you get on consoles I guess. Pushing the resolution and 60 FPS is the only way you can improve on that on a beefy PC that I am sure some people have bought for Fallout 4.