No, I definitely understand what you're saying, and in many cases, I do agree. My dog, for example, doesn't eat packaged kibble.
But, I have yet to find anything solid for ducks, and it's honestly just easier to feed them a good-quality duckling crumble until they're outside. My ducks also aren't free-ranging ducks, so I'm unable to just allow them to eat what they can outside. They'd starve, lol. A lot of people DO free-range, but when you first get ducklings, they're more likely to perish if you just let them free-range before they get in their feathers. After that, they're capable of going outside and free-ranging and practicing a more wild-like behavior.
EDIT:
Also, just to add, keeping them in houses isn't really "natural" either. I mean, take dogs. They wild cousins don't give each other cookies, put collars and leashes on them, or use metal prongs for discipline. There will always be something NOT wild that we're going to do that they wouldn't do in the wild. That's just what happens when we humans decide to domesticate an animal.
I do agree that we should cater to their immune systems and their digestive systems as best we can. I believe that in the wild, they eat these vitamin-rich foods, which is why they don't need to supplement. When we raise them indoors(which is advised for the above reasons) they don't get all these extra things, so we have to supplement that. For us, it was easier to supplement them rather than getting the foods that would have contained all this goodness.