From the factory. Barrel cocking guns can maintain astonishing accuracy and consistency over thousands of rounds. If cocking the gun using the barrel as a lever had any affect on this the guns would be incapable of even reasonable accuracy.
Beeman used to have a service available to gun buyers called "select barrel angle". For a small fee they would, supposedly, go through inventory and hand pick a rifle with closer to level, or no droop, for those people who planned to use receiver sights and scopes. They also had a service called "barrel angle correction". This would adjust a gun's droop for people who had rifles in the field and wanted to add receiver sights and scopes but run out of up elevation. Read "bend the barrel" here. These were the days before a drooper mount.
I don't know if droop was engineered into the rifles or if droop was simply a manufacturing anomaly that had a tolerance attached to it. As said above, the capability to make perfectly aligned parts is not a question. Why they put it in or left it in is a mystery but if it's on purpose it may be to compensate for worn parts as the gun aged. Even that sounds like a stretch to me.