Want to get users opinion on this topic
IMO, If you have a setting that needs to be applied at a “system” level(JVM\CLR\wM products etc) i would make an entry in the server.cnf and use it as an extended setting. If there is a need to access a setting for an application\interface that is built using webMethods custom code i would prefer to use a global variable. An example would be From email address for the server or email hostname which can be used by all interfaces to send out emails.
Yes each has its own advantages and I believe application/system level global changes and so there would be no conflicts! :)-