We're working on adding identity column support for AUTO CDC! As of right now, we recommend adding the surrogate key in the source table before AUTO CDC.
You're correct that MERGE INTO itself is atomic, but if a batch is incorrect but still successfully processed (for example, duplicates, out-of-order updates, or partial data), a manual MERGE can leave the table in a wrong state—and recovery often means truncating and rerunning. AUTO CDC reduces that risk by handling ordering, deduplication, and idempotency upfront, and then uses checkpointing to safely resume if something does fail.
