When certain mongod.conf configuration file settings are set to default values such as below, MongoDB issues a warning for each one, but starts up OK as also shown below.

nohttpinterface = false
noscripting = false

1. service mongod restart
   Stopping mongod: [ OK ]
   Starting mongod: warning: remove or comment out this line by starting it with '#', skipping now : nohttpinterface = false
   warning: remove or comment out this line by starting it with '#', skipping now : noscripting = false
   forked process: 32090
   using syslog ident: mongod.27017
   child process started successfully, parent exiting

I think specifying a default value in the config file should be perfectly legitimate as it reinforces explicitly what the setting is and no warning should be given.