As far as I understand, the only real advantage of HTML5 semantic markup is for search engines and web crawlers to interpret the document better.
Since intranet applications have nothing to do with search engines or web crawlers, what are the advantages of using semantic markup in HTML5?
There is no straightforward example to point out, but the website (even intranet) can be consumed by different user agents (on different devices).
You are probably familiar with Skype (and the iOS Safari) making phone-number-like words clickable. In the future I can easily imagine mobile browsers being smarter to assist the user in completing tasks on the page, like importing a clearly indicated contact to the address book.