One thing it doesn't mean is that OmniGraffle can't do that. I just made a document with a couple of different layers on a canvas, turned off printing on most of them, and exported the remaining one as a GIF file without incident.
Open up the Console application (it lives in the Utilities folder in your Applications folder). Click on All Messages on the left, then type OmniGraffle into the search box at the upper right. Mail whatever is left to
omnigraffle@omnigroup.com and see what they have to say.