Actually, in your example, it was the Countdown team that threw out the continuity. Morrison was planning the whole thing out in every detail - it being very complicated - but editorial thought they could make a buck from a lead-in series, so they asked him for the first issue's script and gave it to the Countdown team; they ignored everything but the bare bones of the stories they were meant to be leading into, instead just doing their own thing and generally sucking at it.
Unfortunately, my scanner is broken, so here's a few textual examples:
* Poison Ivy – his previous non-DCAU story with her consists of her being stalked by a giant plant, possessed with the souls of the people she fed to it (cliche alert), leading to an entire issue of poor excuses for tentacle porn in which she is raped by said plant and develops a phobia of her own freaking powers, rendering her utterly pathetic and useless. Or, in simple terms, she spent an entire issue being raped by a haunted tree. * Catwoman – his major arc with her in Detective reduces her to “Batman’s ex/Woman in Fridge/Woman placed on pedestal”, less than half a year after the final issue of her series said the exact opposite. * Likewise Zatanna – all the character-building and ideas created by Morrison in Seven Soldiers: Zatanna are thrown out the window in favour of a Mary-Sue “Batman’s Girlfriend” based largely on Dini's own wife - which really shouldn't be allowed. * Oh, and the ‘new, improved’ Ventriloquist. I’ve explained this before, but here we go again: The Ventriloquist-Scarface team worked only because it was a juxtaposition of how pathetic Arnold Wesker was compared with his alter-ego; look, for instance, in BATMAN: CITY OF CRIME, where his blank expression and silent demeanour next to his alter-ego gives him an almost frightening aspect. Replacing Wesker with a beautiful vapid blonde woman negates all of the character’s interesting features and potential for scariness, partly because it suggests that Scarface is more of a malevolent spirit than one man’s alternate personality (it is scientifically and psychologically impossible for two separate people to engender the same alternate personality), and partly because it implies that beautiful blonde women are just as pathetic as sad, useless old men. Which is a pretty broad generalisation, no? * …And continuing with that trend, the new Ventriloquist’s origin? “Hush’s Girlfriend”.