There used to be some confusion in the documentation and in the code on what -rn (or the "renumber" field) was supposed to do.

Right now these are the parameters that effect numbering;
"renumber" forces renumbering the equations each time step (which certainly isn't a optimization, but sometimes necessary)
"profileopt" uses Sloan's profile optimization during numbering.

There is no command line version of profile optimization.
You could also have both of these active at the same time if necessary, they are not mutually exclusive.