All the experiments that I have seen done do indicate that only the first link on pageA to pageB passes Pagerank and anchor text. Subsequent links from pageA to pageB don't pass pagerank or anchor text. If either link from pageA to pageB has a nofollow, then Google treats all the links from pageA to pageB as if they have a nofollow.
There is no exception for navigation links. If the first link in a page is the navigation link, then it is the one that passes Pagerank and anchor text.
There is a practical limit to the number of links in navigation. Most sites that I use have no more than 100 navigation links. Only very small websites are going to link to all their pages through navigation.
A few years ago, I viewed internal anchor text was very important. Today, I don't think that is true. Google now seems to place far more value on usability than on internal anchor text. Today you should choose the anchor text that helps the user know what the link is and doesn't repeat information from nearby links, even if that means that each link has less optimal anchor text from an SEO perspective.
Google seems to also be handing out more "overoptimization penalties" in the last few years. These penalties are often triggered by keyword stuffing and overuse. Getting keyword rich anchor text for your internal links can hurt more than it helps.
As far as Pagerank goes, having it passed through navigation seems to be just as good as through links embedded in content. I haven't seen any evidence that in content links are more powerful than links in navigation.
In short, this is the way it works, but it isn't anything that I worry about these days. The way to rank now is to build a comprehensive site that covers all aspect of a topic. Internal anchor text and Pagerank sculpting are SEO techniques of yesteryear.