The E is saying, I think, that canon is what made it to release. The little inconsistencies like that are now forever a part of the game universe. It's too late to go back on them, we have to live with and justify them instead. (Or just throw them the **** out and say it was for the good of the story, but at least admit we're throwing it out.)
That and the fact that the Shivans are (admitted by FS2) constrained by the same physical laws means that while their systems may be laid out differently, on a subject like how to determine optimal pulse repetition for accurate information on a moving target the governing factors are in the math, not the psychology.