Version 1.3 of Take Control of DEVONthink 3 has just been released, containing all the good stuff of DT up until version 3.5.2., including e.g. the recent surprise release of ScanSnap manager.
I’m not sure whether the DT staff will update it on their website as well, but if you’ve acquired the book through the Take Control website, you can download the new version in your account as of now.
Personally I would endorse the Take Control book as a companion to the manual, as it’s more descriptive by nature and contains many tips. And while I am at it, please consider taking a look at the other books in this series as well such as Take Control of Backing Up your Mac.
Happy reading and thanks to @joekissell for the update!