grdconvert is used to extract a 2-D grid from a multidimensional matrix. However, it is not going to write 1-D arrays for anything but the longitude and latitude (or x and y) dimensions. Thus, while the multidimensional file may have 1-D vectors called time and altitude for those two dimensions, these will never be written out since the grid that is written is for a single value of time and elevation.
Where did you read that it will also write out information about time and altitude? I can then fix whatever is not well explained there. Looking at our documentation, I do not see any discussion or examples where anything but integer indices are passed via [ ] and values passed via ( ). When you say (time,lev) I cannot tell if you mean you typed that verbatim or if these are actually something like (2018-12-12T,3500) or whatever.
As for the odd final error that seems like a GMT bug. Might it be possible for you to share the MERRA2_400.inst3_3d_asm_Np.20180101.nc4.nc4 or point me to it?