Fwiw, the brand of noodle matters. I don’t get congee, i get nice distinct noodles, they are just soft and taste deliciously of broth. And if i didn’t overcook the beans, the remaining broth stays clear. (I often overcook the beans and get muddy broth, but that’s definitely a bean issue, not a noodle issue.) I’ve never had a problem with the broth getting cloudy from noodles, it just gets sucked up and disappears.
My husband often cooks the noodles separately. He makes pasta e fagioli and serves a pot of soup, a pot of noodles, and a bowl of grated cheese. His noodles just tastes like noodles, not like broth. (And his broth is less clear than mine, because we use different beans and different cooking techniques.) He cooks them separately partly because it’s faster, and partly because he wants his soup to stay soupy.