In both the sentences, "By the.." indicates "Just before the time approaches or during that specific time.." "By the end of winter..." means "Just before winter ends..." "By the year 1600.." means "During or before the year 1600..."
It indicates that when you reach that point in time, the other thing has happened. It could have been immediately before, or it could have been hundreds of years before.
I'm not done yet, but I'll be finished by the deadline at 5 p.m. Don't worry.
You don't konw if I'll finish four hours before the deadline or at 4:55 p.m. Y