Predefined commandlines are only specified in the game once. You don't need to create it for each client.
I thin that the combination of predefined commandlines + custom commandlines does what you want.
In the game's details create 3 predefined commandlines:
CTF profile
TDM profile
WAR profile
In config files create server_ctf.cfg, server_tdm.cfg, server_war.cfg. Each predefined command line executes its own file
Common features can be in global.cfg to avoid configuring hostname, rcon etc more than once.
In server_ctf.cfg, server_tdm.cfg, server_war.cfg the first line would be "exec global.cfg", then all the specific cvars.