Well, there were clear indications in the first couple of chapters that Birthright was supposed to be set in the present day, or at least more present day than Man of Steel was. It also clearly and blatantly contradicted post-Crisis continuity, and not in the fanboy quibbling sort of way either. We're taking major contradictions.
The references to Birthright started popping up at the behest of Eddie Berganza. For example, Jim Lee told of a story of how, when he drew "For Tomorrow" he initially used the Byrne models for the Kryptonians but was directed by Berganza to use the Birthright models instead.
My feeling is that it was supposed to be an Ultimate/All Star-type story that simply got shoehorned into canon by Berganza. That seems in line with how poorly the story was executed into canon, as well as how quickly it was jettisoned following Infinite Crisis.