When client's have an SSO portal that only allows individuals to log into WF via a link on their portal, there are some notification complications. If that user receives a notification with a link to the object in WF, and they click the link, they will get an error message because the native link in WF does not have the information appended to it that would inform the SSO portal on where to send the user. This is regardless of whether or not the user is logged into WF. This is a complicated scenario but a very real scenario. So, it basically devalues the communication coming out of WF.
The fix would be the ability to do deep linking. In other words, in the notifications area the option to add a suffix or prefix to the native url that is being sent out via the notification. I think this warrants additional discussion with more technically savvy individuals, which I can facilitate as needed.