Sorry for the delayed response. Regarding using the equivalent index option, I quote from this post which presents detailed instructions for using and setting up the override mesh object in FDTD:
"In most cases, FDTD uses the number of points per wavelength for meshing. The larger the refractive index of a geometry, the smaller (finer) the mesh size. So, the equivalent index will depend on how small you want your mesh to be in the override region.”
Therefore, in this method the mesh accuracy is no longer static and changes as the mesh accuracy slider is altered, which could be advantageous for convergence testing.
Changes in simulation time is expected as the trade-off for having a finer mesh is an increase in computational requirements. That’s why performing convergence tests is an effective approach to determine the ideal mesh settings (as opposed to simply using the finest mesh possible).