Configuration keys are used to be able to add config informations to different areas which you can use in the flow, it can be some value you need to have on a partner to lookup in some external system, it could also be on a document config to be able to overwrite certain values if their set on the key.
there are a set of system configuration keys that can be created and they will do something in the flow as well you can read more about that here.
[Should there be more typed here about how to configure with all the different type and groups etc?]