I've never run the Windows defragmenter and Defraggler literally side-by-side, so I don't know if my experience will be useful, but for what it's worth...
Until recently, I had Windows defragmenter set up to run weekly defrags on my 1TB data disk automatically. I didn't pay much attention to it, in fact, I'd forgotten that I'd even set it up. But I would run Defraggler manually every couple of months (when I thought of it, basically), and invariably got readings above 10%. I'd run Defraggler manually, and knock it down to <= 5%.
Then a couple of weeks ago, I finally switched and started using Defraggler to do scheduled runs instead of Windows. When I checked the state of the HDD manually with Defraggler a couple of days ago, fragmentation was down to 5%. So superficially at least, it appears that Defraggler is doing a better job.