Of course defragmentation, and more to the point, optimization, or strategic placement, can indeed improve performance. Doing it the right way can also reduce the strain on the disk. Only excessive and unnecessary defragmentation/optimization is detrimental. If you want to read some more I recommend the pdf manual from UltimateDefrag4 by DiskTrix, available here:
http://www.disktrix.com/manual.php
Now, depending on your computer's specs and the usage you make of it, you may really not feel much difference between Windows' own and 3rd-party defraggers. But in some cases the differences are immense. I'll recount one experiment I made and you'll see what I mean. Of course, anyone can reproduce this.
Take a number of files, in this case it was over 11,000, sized (if I remember correctly) up to a megabyte each, mostly a few kB only. I sorted them by name with a custom MyDefrag script, and then measured their read time with Raxco File Access Timer. Then I randomized their file names with some renamer, I don't remember which now, and did the measurements again (at least 3 times each, o/c). With randomized file names the read time more than tripled (from about 50 seconds to 160)! So transpose this situation to a large image gallery, for just one real-life example of how optimization can improve performance.
You don't even need this type of sorting for performance gains, just placing relevant data together can do a lot. That is, putting all the files from your most-played games, or your everyday work apps, or both, close together in the same (outer, faster) region of the disk, thus reducing the distance the disk head has to travel to read all that often-accessed data.
About boot defragmentation, it affects mostly those locked system files. MyDefrag can't defrag some of them, like many defraggers, but it can defragment the MFT, which Puran does only on boot defrag. I think the files MyDefrag leaves fragmented don't really affect performance (I would assume they're loaded into memory during Windows use).
I hope this helps. Thanks.