The message happens when ioquake3 client from July 29 2011 or later connects to a server is based on ioquake3 source code from July 12 2011 to before July 29 2011.
In order to connect to the server, start ioquake3 from a command prompt, shortcut, or batch file using:
ioquake3.x86.exe +set com_gamename ""
This will allow connecting to all servers.
Drawbacks include not being properly separated from standalone games and if you host a server it probably won’t be listed on the official Q3 master server. For general quake 3 player usage, clearing com_gamename is fine.
It’s possible to fix this in the ioquake3 client but it seems odd to add hacks for a server protocol that existed for 17 days, six years. It kind of haunts me though.