Is there any single-source document that explains the game in it's current state?
The manual is pretty good, though no single document can capture the detail in GC3.
The trick until recently, was finding the manual. Many links point to the long-obsolete 1.03 version, which I suspect is the one you're looking at. The current version is _2018. With the 3.8 update, the manual icon on the game main menu screen (lower right) will bring it up in your default browser.
Or you can find it in your local installation directory, which might turn into a snipe hunt since Steam buries its installation. So a search for GalCiv3_Manual2018.pdf might be your best bet.
Now that you've found the manual, what section should you refer to? Depends on what you have installed and running.