See the discussion at: http://www.nabble.com/Jira-SOAP-interface-and-remotely-updating-custom-fields-td22421561.html

Remote API (SOAP or rest) needs to be able to update all fields associated with an issue independent of screen configuration. There are many use cases for automation being able to do things that are not possible to end users.

A specific case is having a field that is replicated from an external system and any edits that would be done by users would be overridden on the next update from the external system.