Currently, diagnostics are saved with the z coordinate for the vertical direction. This is the simpler, because the CliMA simulations are not ran with pressure coordinates.
To facilitate saving diagnostics in pressure coordinates, you can do something similar as in ClimaAnalysis (see to_pressure_coordinates). This involves knowing both the ClimaCore field of interest and the ClimaCore field of pressure, regridding to an array whose dimensions are lon, lat, and pressure (if the space is 3 dimensional), accumulating regular arrays instead of ClimaCore fields, and saving the array as the diagnostics after any post processing step (e.g. dividing by the number of steps to compute the average). However, this can be pretty slow, since an interpolation is needed for every compute step of the schedule.