Interesting question! I can’t think of any cases where they are directly interchangeable. In general, ‘over’ talks about the result, ‘throughout’ the action.
First, ‘over’ can be used for definite time periods.
I painted my deck over the weekend. (There is a change - deck unpainted to deck painted)
Over the years, he’s become more conservative. (Indefinite time period, changed status - less conservative then to more conservative now)
She won more grand slams over the course of her career than any other woman in history.
She checks Facebook throughout/during the day. (That’s what she does)
Throughout her childhood, she went to church every Sunday. (Action)
Over the course of her childhood, she went to church 700 times. (Some may drop ‘the course of’ here, but it sounds less accurate. Result)
Over the years, I’ve watched a lot of television. (Not ‘I watched. I’m talking about the result )
She won 15 grand slams throughout/during/in her career.