As to biographies excluding some children. I have noticed that does happen. Alexander Alexandrovich is omitted quite often in bios of Nicholas II and even his parents. And as someone else said, sometimes he is listed as having been born before Nicholas, but I think that is how some biographers like to see it because Nixa died and Alexander III became heir and if Alexander Alexandrovich had been born first and then died the chain would look unbroken.
I have several biographies of Alexander III and Nicholas II were Alexis Alexandrovich is unmentioned. Even on the family tree page, his name does not appear. And he certainly didn't die young. Probably because he had no children and so did not leave any family behind to carry on that particular line.
And if the Romanovs were avoiding the use of "Alexandra" then Nicholas should have let Alix go with Ekaterina as she wanted to. Maybe that is the jinxed tie in.