I am using scripted authentication with the bundled script and am wondering which user/password combination will take priority if it exists in both systems?
If you have a user that exists in both the scripted authentication system and the Splunk authentication system, the Splunk authenticated user/password will take priority. An example of this situation might be the "admin" user. Note that in 4.1.x and later, Splunk will authenticate users in both systems.
Similarly, if you are running LDAP auth and Splunk auth, the LDAP user's credentials will be used instead of Splunk auth.