Logical Order in a "manifest" vs in "content"

I’d like to explore the idea of why we need logical order specified in the manifest (or metadata, but let’s just say manifest for now).

As I understand it, the reason is to provide a UA/RS with the ability to provide its own navigation experience outside of any content-based navigation.  I have heard (but don’t fully understand) that it is especially important to AT solutions.  I am correct on these things?  Is there any other reason it is needed?

But I think we would all agree that it is not well aligned with normal web content navigation, where the content itself specifies the navigation (usually via links) and that users have no problems (either with or without AT).

So what would be the downsides to moving to a “content provides navigation” model?  Wouldn’t it enable us to get rid of the complexity (and non-web-aligned) of having a specified order?

Discuss!

Thanks,
Leonard