An integrated Mod Manager as part of the Total War: Warhammer launcher is still in the works, according to Creative Assembly. Responding to a query on the TW: Warhammer subreddit, CA’s Darren confirmed that its development was discussed at the November 2016 ‘mod summit’.
At that event, “the development manager behind the web team discussed with the modders the features they most want to see from a new mod manager / launcher.” Load orders and grouping were reportedly discussed, as well as “version control for incompatibilities”.
Darren goes on to say that the Total War: Warhammer team are in the process of creating a new launcher. There’s “no finite date” on that yet, but CA insist that it will still be happening.
The Mod Manager was mentioned as a “day one” feature in this pre-release document about mod support. That evidently never came to pass, but it sounds like that aspect is still planned.