If the tech tree doesn't agree with the scripts, that's because it reflects the current development version, not the release version. It shouldn't really be included with the release versions anyway, until the game is complete.
Still, I dislike the multi-page tree. It's hard to read, and it's not clear what everything means, despite the legend (which is only shown on the first page). I find it confusing, and I helped MAKE the tech tree.
As for the PDF manual not existing, that's true. Unfortunately, the manual is not being maintained, and the current sources are out of date. Including it would mean including conflicting information, so it's better not to. If someone would maintain it, that'd be different, but it's a rather big task.