Pretty much. There's a strong anarchist culture in Berlin. And while I'm sure the people described in the article are very nice indeed, there are areas where any police intervention is very unhealthy for the police.
It sounds like for this particular story, people actually signed a (very cheap) lease with the owners after the fact, but there are quite a few buildings that are simply occupied.
(Keep in mind that a lot of buildings also have rather unclear ownership records. And if there's no clear owner, there's much less incentive to evict squatters. Why risk it when it then might turn out it's not even yours?)
Especially in case of unclear title it's a good thing to have the building occupied as a squat. It prevents further detoriation of the building and urban blight in general - the occupants will see that the roof is tight and that the windows remain whole. Whoever owner there is may lose out on the real estate, but an abandoned building isn't worth much to begin with, and the city benefits at the end of the day.
It sounds like for this particular story, people actually signed a (very cheap) lease with the owners after the fact, but there are quite a few buildings that are simply occupied.
(Keep in mind that a lot of buildings also have rather unclear ownership records. And if there's no clear owner, there's much less incentive to evict squatters. Why risk it when it then might turn out it's not even yours?)