We consider a random Gaussian ensemble of Laplace eigenfunctions on the 3D torus, and investigate the 1-dimensional Hausdorff measure ('length') of nodal intersections against a smooth 2-dimensional toral sub-manifold ('surface'). A prior result of ours prescribed the expected length, universally proportional to the area of the reference surface, times the wavenumber, independent of the geometry. In this paper, for surfaces contained in a plane, we give an upper bound for the nodal intersection length variance, depending on the arithmetic properties of the plane. The bound is established via estimates on the number of lattice points in specific regions of the sphere.