Snapshots. Both 'Stop' and 'Snapshot' backup modes use the Snapshot-feature of the underlying storage. That is the reason why the downtime is low for the Stop backup mode.
The 'Stop' mode initiates a shutdown of the VM, then makes a snapshot followed by a reboot.
The 'Snapshot' mode only signals the OS to clear its caches, and then makes a snapshot.
Generally most OSes these days work well with Snapshot mode if you install the QEMU guest agent (and activate the agent in the VM options). The 'Stop' mode is safer because it guarantees file system integrity at the cost of a small downtime (and other things, like not being able to use the dirty-bitmap speedup feature).