APM Rewrite and MS Sharepoint

One of the reason for the cookie based persist because MS Office opens a different connection back to the server.

That's absolutely at least the primary reason for requiring persistent APM session cookies with SharePoint. Because APM is cookie based, and because documents are generally opened in an application separate from the browser, you need a persistent (file-based) cookie that the app can access, something that's outside of browser memory. It's also safe to say, that there are exceptions to this rule, that some tools can use the browser's in-memory session cookie, and some that can't even use the file-based cookie. It tends to depend on which SharePoint version, which Office product is installed on the client (if any) and/or which app is used to open documents, and what day of the month it is...