It is generally a good idea to run with auto commit enabled. Using any transaction framework will always automatically disable auto commit for the duration of the transactions.
When running simple SQL statements relying on auto commit requires less round-trips to the database and thus shortens also the time locks are held in database improving scalability.
Of course not every database operation can be written in single statement and then transactions need to be used. nFlow uses them only when needed to for correct functionality.
There are lots of risks if auto commit is disabled and the application runs statements that modify the database outside a transaction framework. I've seen a large project where there were occasional updates and lots of reads. It took a long time to debug a case why the db reported a deadlock for two items that were touched many minutes apart. Root cause was that @Transctional annotation was missing from one place.
If you have a use case for running with auto commit disabled I would be very interested to hear. If there is a valid need, it will be of course possible to make nFlow allow disabling auto commit outside of transactions too.