No, it literally says the law says you must seek permission if you wanna leave for more than 3 months and the govt must always grant you this if not in a war. And if you fail to seek permission nothing happens. You can ignore it without consequence.
The consequence is you violated the law, and they can have you at any time, even retroactively, for that.
That they don't is merely a detail. If it really has "no consequence" they should remove it.
And no, Germany does not allow retroactive criminal punishments. That’s more something that happens in Russia, China and probably soon America