It depends on what you are trying to achieve. I can't speak for VMod or GMS, but both Groundwater Vistas (
https://www.groundwatermodels.com/) and AlgoMesh (
https://www.hydroalgorithmics.com/software/algomesh) have tools for creating layer-dependent discretisations in the form of spatially-confined vertical sub-layering and/or cell pinchouts. In AlgoMesh, for example, vertical sub-layering is done by setting up explicit Lateral Connection Groups (LCGs) - see section 5.3 of the user guide here:
https://dl.hydroalgorithmics.com/AlgoMesh%20User%20Guide.pdf
Layer-dependent discretisation in a more general sense is problematic in layered prismatic grids like those used in MODFLOW-USG. If you think about the geometry of any partially-overlapping cells, e.g. in a quadtree/octree grid with four cells on one layer and a single cell covering the same space on the layer below: whenever you have this interface between two adjacent layers where the elevations are not flat, there will be an overlap in cell volume. This is a problem because the model will effectively double-count any such overlapping volumes. The problem could be avoided by introducing an additional "buffer" layer on the upper side of the interface which repeats the fine mesh but has a uniform bottom elevation - but of course you are then adding potentially many more cells, which may eliminate the benefit of going to a coarser grid for lower layers anyway. Perhaps it could be effective in some settings. However, I suspect creating this sort of grid would be difficult in most, if not all, existing graphical modelling interfaces. An appropriate DISU file could be set up manually (or by a custom script), as a merger of multiple independent DISUs created by GUI for each of the different grids, by an appropriately adventurous modeller!
Regards,
Damian Merrick.
Disclaimer: I am the author of AlgoMesh.