The better way to display your call logs rather than having them mixed in with all of your emails is a very easy ALT+P keystroke from your inbox. Also, this gives them to you only when you want to see them rather than all the time. This is better than having them always present and mixed with emails primarily because missed calls are displayed as unread messages. Poor design on RIM's part in my opinion.
The guide was written in response to a thread here where the user wanted to have it display the same way it did in the 3.7 firmware...
I think it's a matter of personal preference...
Mine is set up like this:
Phone --> Options --> General Options --> Phone List View = Call Log
Phone --> Options --> Call Logging = Missed Calls
The phone app will display the entire call-log and only the missed calls will be displayed in messages...
To each their own I say