I thought it was released separately. I've the Dr. Manhattan BluRay box so will check when I go home. I certainly haven't seen The Black Freighter mini-movie anyway.I find it really difficult to watch as the scenes match the comic so closely I'm constantly taken out of the story in admiration at the technical achievement. No matter how much I try I can't "unknow" the comic in order to enjoy it properly as a film. The subtlety of the comic didn't translate well to the big screen in my opinion and some of the dialogue seems corny. It's ok, and as you say they did a decent job of compressing all that source material into a commercial movie. I have it on DVD but every time I watch it I get distracted and end up doing something else instead.
I heard there was an animated version of The Black Freighter comic story that was included with the original deluxe DVD but I've never seen it.