Ubuntu does not use the standard pg_ctl for postgreSQL. Instead, it uses pg_ctlcluster.
That in turn controls the different PostgreSQL clusters. When you do an install of a new cluster, pg_ctlcluster is smart enough to put postgresql.conf & pg_hba.conf into separate dirs.
So to be specific, /usr/lib/tmpfiles.d/postgresql.conf is just a tmp file that you can ingnore, /etc/postgresql/9.4/main/postgresql.conf is the original version for the 9.4 cluster and /var/lib/postgresql/9.4/main/postgresql.auto.conf is the actual, live version of the 9.4 cluster that you need to change to affect the 9.4 cluster. Likewise for the pg_hba.conf.