That would be a very incorrect assumption. Odds are, if there is any kind of command line tool for Windows Update, then the graphical version is just a front end around that program. Why would Microsoft go to all the trouble of creating two separate versions when they can just create a program that runs the command line tool, traps the output and formats it in a more aesthetically pleasing way? Why duplicate that effort, especially if the command line version were somehow always superior? That's a completely false assumption, but even for the sake of argument, it makes no real sense.
Even assuming they did reimplement the program twice, they are still both comparing the current state of the system against the same list of available updates, so I again don't understand why it is you'd expect the results to be any different.
You have two sets of data, one being the updates applied to a specific system, and then the master list of all available updates. No matter how many different programs you have parse that data, you're going to wind up with the same results.
Note: This post was edited by a forum moderator to remove some unnecessary text on 04/15/2012 at 8:52 PM PT