As opposed to config_file, hba_file, etc. the name and location of the autoconfig file is fixed to $PGDATA/postgresql.auto.conf (guc.h)
The static name also appears in some other locations, such as pg_basebackup, pg_rewind & initdb.c. New feature suggestion: Allow to set the file's location, as with hba_file and ident_file. Would be glad to make it my contribution to the code.