I do not believe you can run autoconfig for database server. Oracle apps database are configured with some specific table which are used by these adcfg pre clone scripts to store some information but you do will nto find these tables in normal databases. This is the reason I believe you cannot run autoconig on normal databases.
You might be able to do something similar to autoconfig if you show some creativity by tweaking the scripts and creating the tables but why to go this difficult route. You can instead create and automate script for duplicating database using RMAN.