The point of defragmentation in this context is to recover fragmented disk capacity as contiguous free disk capacity (free space).
That's the major objective in terms of extents as you have mentioned. Another thing is if a file is highly fragmented the drive may have to work a bit harder to find all the pieces, slowing things down a bit.
Do you have any reflections on what happened?
Probably pretty much as you said. Simply having ST copy the files elsewhere on the drive as part of defragmenting resulted in some of the file chunks between empty spaces being moved elsewhere and the space made contiguous. That's why I saw a slight improvement in 1-100MB free spaces simply by the movement of tiny file pieces allowing some of those tiny spaces to now become contiguous. Still, if the the space is also broken up by some unfragmented files Speed Tools doesn't do anything to them so the space remains broken up. Hence I still had 17,000 <1MB free space pieces with only 200 fragmented files. It was probably unfragmented files staying put that was still breaking up the space. It's not until you force those files to be copied that the simple process of copying ends up with them being placed contiguously and all tiny spaces made contiguous.
I don't know the details of drives and file systems. For some reason those final files weren't defragmenting until I truly made a large contiguous space by cloning. Maybe some of that pre-cloning contiguous space was reserved by the system and wasn't available for defragmenting. After cloning there truly was space available and the final defragmenting run defragmented all the rest of the files (with the exception of a few active system files since I was running it on an boot drive). I still wonder why they weren't copied on unfragmented though.
Not that I'm in a rush to try it, it would be interesting in seeing how effective cloning alone would have been in terms of defragmenting the files. For the files remaining after using ST the cloning process defragmented only about 70% of the files. There wasn't anything special about the remaining files. Some were mp3s, one was an application, one another media file.
Edit comment:
When I first started using ST defragmenter I had about 1600 fragmented files. I ran it a couple of times in succession until it wouldn't defragment any more files, and there were still 1000 fragmented files. Every time I deleted a large file (e.g., a 2 GB sparse image) it would go a bit further. So it is effective, but definitely won't go all the way on its own, especially if you really, really want to keep all your files. 🙂