I strongly support these observations.
Another usability problem (real for me) is the section title.
On the reader mind, the HTML title of the first result become the "section summary"; in the Yiin screenshot, the standard user thinks that "Filtering on relations breaks pagination" is the title/matter of all the links below from github.com... and obviously isn't true, but it's misleading.
Another thing I thought was "is this more important than others? does this link has a parent-child relationship?"
You can see that this is a modeling problem, not only a usability one.
If you'd have to choose only beetwen grouped and ungrouped...I'd surely go for "ungrouped": this is the common experience, has a simpler mental model, is lighter on resources for the project, has an immediate comprehension. Last but not least, it's also open to add a "result grouping" setting for people when and if you'll decide to.