The more I think about the non-Black Sparrow covers the more it seems to be a non-issue. When many of us started reading Bukowski (those many dusty years ago) and Black Sparrow was the only game in town, the books were like little secrets, and the quality and unusual design only made you feel more like you were in on something really unique and special.
But I don't think that Bukowski can really be looked at in that light anymore. Born Into This and Factotum are showing on a cable movie channel somewhere every week, and Ecco is dropping the books into every book store on the planet. Bukowski has gone mainstream. Small "m" mainstream, sure, but the name is out there, and the dirty old man persona is out there, and the repackaging of the books was inevitable at some point, no matter what.
Bukowski and Black Sparrow will be forever intertwined in my experience, but people coming in to the party now aren't burdened with that. ;) And really it's the words that matter. As long as they don't fuck with them, who cares what the wrapper looks like.
I have some hideously covered versions of Herman Hesse (and fewer - though equally unfortunate - Mark Twain) books, but I didn't really pay attention to the covers when I was a young sprout reading that stuff. The covers were irrelevant to me. And that's probably how someone coming to Bukowski now looks at it. As they should.