No, the command line does not provide commands for creating the Message Suppression Rule File (.SRF).
To work around this problem, follow these steps:
a. First, generate a (.SRF) file using the GUI.
b. The (.SRF) file generated from the GUI should contain the messages you plan to suppress.
c. The instructions executed from the command line for a full compilation will read the (.SRF) file.
d. The generated resulting (.rpt) files, such as .syn.rpt, .fit.rpt, .sta.rpt, etc., will no longer show the suppressed messages.
This information will be added in a future release of the Quartus® Prime Pro Edition User Guide.