+g_motd MOTD only works if you first add
seta g_motd "CREATE THE CVAR" to /home/USERNAME/.q3a/baseq3/q3config_server.cfg. See solution 3 below.
Any one of these options should allow you to set g_motd. If one does not work, please try the others.
Solution 1. Use
+set g_motd \"MOTD 123\".
Solution 2. Rebuild ioq3 git master and use
+set g_motd "MOTD 123" or
+seta if you want it archived instead of having to be set at start up each time.1
Solution 3. Start the server and run
seta g_motd blah in the server console then quit. In the future you can use
+g_motd MOTD 123.
1 You really only need to run
seta g_motd blah once, which adds it to q3config_server.cfg. It keeps the archive settings later even if you use