The supposed goal of CoIE was not to unify all DC outlets across all media, and it can be argued the plan wasn't even to unify all of DC's comics in one universe. Within a year of CoIE, DC published both "Watchmen" and "The Dark Knight Returns", both destinctly set outside of the ongoing DC Universe, and both most likely in the works while CoIE was still going on.
But the goal WAS to unite all the various comics lines and "universes" that had crossed and connected over the decades, including comic lines purchased from other companies (like Carleton), into a singular continuity. That's why, after the Crisis was over, DC published a 2-issue series called The History of the DC Universe, to set down how all of the historic characters and events fit together, and what the canonical origins of many of the major characters now were.
Did that mean that all of DC's output then fell into that singular universe? That no alternate takes on characters were allowed? No, of course not. There had always been, and would continue to be, DC titles that weren't tied into the greater DC universe -- funny animal/people books (Captain Carrot, 'Mazing Man, Hembeck Destroys the DC Universe), external crossovers (X-Men/Teen Titans), Elseworlds, some of the Vertigo titles, and yes, Watchmen and The Dark Knight, as you mentioned. Even when some of those titles had appearances by mainstream DC heroes, they generally weren't considered to be in continuity with the greater mainstream DC universe.
But DC leadership very definitely wanted all their mainstream titles firmly located in the same universe, with the
multiverse banished -- no more Earth 1, Earth 2, Earth C, etc. That was
explicitly stated.