That's indeed how it works. The tree is created dynamically, no actual branch or leaf positions are stored.Good idea would be make position in tech tree absolute only for first tech in tree. And rest depend on (first) parent. This way if you want to add technology in the future, you can easily modify tree. and move tech trees or whole branches of scientific topics if necessary.
Yep, items haven't really been focused on, most of them are from pre version 0.1. There should be some new ones coming soon though, now that the tech tree and most overworld systems are in place, there's even a sneak peek in the latest devlog.I guess item design was not even part of development yet so probably it this post not really that important just yet, but still writing what I felt while playing.