When the ocean model is run, it uses one of these grids (gx3v7, gx3v5, etc.). In order to match this grid when running the diagnostics, you'll need to know what grid the model output you are using is. Many of the changes between different versions (v3 vs. v5) of the same grid are changes in bottom topography or land mask changes (though there could always be other changes), so yes, there is a reason for the name change. You could still run the diagnostics with a different version than your output, but you might end up with some strange points in the difference plots with observations based on these grid differences.