Watch the text in the box. Your "Received" will be very low (not zero from what I've seen, seems they always hold some key file until the actual patch) - that's the only thing you're actually downloading. The Patched count is just how big the modified files are - it'll go up even if it's copying from the prepatch or from the tribble/holodeck folders, but your received count won't go up while it's doing either.
The prepatch download doesn't apply the patch directly to the game, because then you'd get a version mismatch and not be able to log into the game at all until the patch actually went out.
Their 'patch' progress leaves something to be desired, but yes, the amount that you are actually downloading (the recieved) will be considerably lower than it would have been if you had not pre-patched.
As for why pre-patch is done; I believe it is more along the lines that a portion of the users will pre-patch before it goes live, reducing the number that will hit the patch server when the new build goes up. Players tend to login to check out new major updates and that can overwhelm the patch servers creating delays for everyone.
Apparently for no good reason, I am currently downloading a patch for holo and amazingly it is exactly the same size as the prepatch I did yesterday
So exactly when does the prepatch get used??
The patch gets used at the same time as everyone else that is all anyone really needs to know. The developers and development goes how it needs to go.
Are you actually complaining? Seriously please say your not complaining that your computer and broadband needs to complete a small download and turning pre-patching into a negative thing instead of the positive feature that it is.