The flicker noise is dependent on the drain current cdrain, which is a function of Vds and Vgs (in forward mode, Vds>0 -- or of Vgd and Vsd in reverse mode), so it is not surprising that you see a dependence on Vgd.

The simplest flicker model in bsim3v3 is NOIMOD=1 or =4, where the power spectral density is KF * |cdrain|**AF / (Cox*Leff*Leff*f**EF)

The more complicated NOIMOD=2 or 3 uses parameters NOIA, NOIB, NOIC, and also depends on cdrain.