Yes you're able to have all configurations for a file converted to individual .step files.
To accomplish this you'll need to make some small changes to the task.
Within your task navigate to "Conversion Settings"
Under 'Configuration to output' Select "All configurations"
When this task then run it will output a file for all configurations of a part.
I also generally uncheck "Allow user to change this setting" at both places in this page.
This is because it will prompt a user for what configurations should be exported and tasks are generally an automated process.
That is to easy! I bet I would have seen it if I would have looked.
I might keep that "Allow the user..." box checked, for reasons. Unless the users start not wanting to deal then I'll turn it off.