This article of mine reviews the issue of the effect on flow of structural dip, its related vertical anisotropy, and related limitations in MODFLOW:
Note that it cites this paper on the two choices a MODFLOW modeler has for grid design: the "grid overlay method" and "boundary matching approach."
Jones, N.L., T. J. Budge, A.M. Lemon, and A.K. Zundel. 2002. Generating MODFLOW grids from boundary representation solid models. Ground Water 40, no. 2: 194-200.
Though perhaps not using these names for the grid design, Mary Anderson discussed this in both her modeling courses at the University of Wisconsin, and her textbook.
GeoSolid3D sets up models using the "boundary matching approach."