It is true, there are points outside the Voronoi geometry. While I can't say for certain, I think it's because that some or all of the cell planes associated with those points are completely unbounded, so the script has no way of representing them as faces.
I used Selection(free) on all the previous examples. Selection (Bounding Box) was an attempt to reduce the number of unbounded points by adding "invisible" points at all the bounding box corners. In general, it doesn't really work.
All the points are construction points, yes.
I would like to see better 'enforced' bounding, absolutely. And I suspect that it's probably possible, but probably requires a lot more math than I've got in there now.
For dealing with "old" data, I suspect the script could be updated to actually delete the 'results' file where the Qhull output is placed before every run.
As for why you aren't getting results with your LSystem data, I'm not sure. If you want to post a scene I can take a look at it. If it's a ruby issue, I'll try to do something about it. If it's something inside Qhull, there won't really be much I can do.