Phone/jack connectors have been around since the 19th century (!!!!!), I think we'd know by now if they broke computers.
I am very surprised that nobody at Apple could have better foresight to include the ability to choose between 2 different audio outputs. Even the people at Microsoft were smart enough to think of that lol
It's actually got it's use. For example late at night when you want to make bloody sure that sound only goes out headphones and not speakers. If you want this to work differently, hit the Apple feedback links and tell Apple what you want.