When using Goldengate to instantiate target database from an Oracle source database, replicat process can be started to coincide with extract based the method used for instantiation, e.g. RMAN or datapump.
ATCSN is used to start replicat if RMAN is used to instantiate target.
From Database Backup and Recovery Reference, UNTIL SCN specifies an SCN as an upper limit.
RMAN restore or recover up to but not including the specified SCN.
AFTERCSN is used to start replicat if datapump is used to instantiate target.
The export operation performed is consistent as of FLASHBACK_SCN.
Hope this helps to clear up when to use ATCSN versus AFTERCSN.
Oracle GoldenGate Best Practices: Instantiation from an Oracle Source Database – Doc ID 1276058.1