I think there was a suggestion Dark Glass was a project by the Dominion to break into the Webway and either use it to attack the Old Eldar Empire or enforce mutually assured destruction so the eldar would stop raiding the Interstellar League.
There was also the Corrupted Man of Gold to add to the list, the Man of Gold who got spat out by the Warp as a crazed Cenobite/Dr. Weir nutjob controlling a high-end DaoT ship who started immediately firing on everyone. After a prolonged struggled the Grey Knights finally brought it down and its death screams cut off the Astronomican for a bunch of worlds. The canon version of events was supposedly mentioned in the 5th Ed. Grey Knights codex, but we weren't sure if it was referring to the Cacodominus.
A whole Dark Age/Golden Age faction might be a little much for the balance of the setting. Most factions aren't playing at their full potential. The Imperium doesn't have access to all their DaoT tech. Neither do any of the eldar factions. Orks are limited by how much WAAAGH! energy there is, and even then some of the subtler ideas the Krork came up with are lost. Necrons lost two-thirds of their forces during the Great Sleep. Tau are playing catch-up. The only one who are really batting at full strength are tyranids. A DaoT fleet would blow everyone except Necrons and tyranids out of the water. Imagine an entire warfleet of Ark Mechanici, not just using them as a bunch of capital ships.