So, storing some thousand entities in a single transaction takes a
little more than 1 second, while running each put operation in a
single transaction takes ~50 seconds.

For the record, I'm more concerned that storing "a few thousand"
entities in a single TX takes  a full second: that's not expected, but
my guess is that in this specific case you're not warming up the JVM
nor repeating the test. Having batching enabled, I'd expect this to be
in the order of millions / second.