If I understood correctly, you use the login to verify the account information and to check whether funds are available. The transfer is initiated via ACH.
Sofortüberweisung doesn't use ACH (or SEPA), they actually transfer the money via Online banking using a bot pretending to be the account owner.
It's popular because SEPA transfers are really cheap, compared to paying with credit cards.
Last time I paid with SOFORT I noticed that they hadn't committed the wire transfer. KLM issued me with my flight tickets, but the wire transfer was sitting in the outbox and could have been cancelled. Not sure what happens if I cancel a payment like that - does the merchant get notified and cancel the flight tickets too?