The 3d extent for grids and levels when associated to a scope box appears to have a default offset. It does not look like there is a way to modify this in any version of revit....
There is the option to manipulate the 2d extents. This can become cumbersome.
I do not know if this is a setting already in Revit that can be changed.
I would like to see an option to customize this default setting.
My idea would make this offset from scope box / 3d Extents an option for the System families of Grid Types.