I think it is the same reason a lot of their breeds get ruined or get crossbred. Ideal once sold real Madagascar Game from an actual breeder, I believe from Georgia, but since Madagascar Game don't lay enough eggs, like any other breed, they crossbred it to a better producer who looked somewhat alike. In their case. Turkens. So in the end, their games are now just a really ugly Turken. (no, I don't think Turkens are ugly - but the product they made sure is!) And with Araucanas and Ameraucanas, I believe they just weren't getting enough sold, and the Araucanas weren't doing well enough. So - They crossbred them. Also, you get more buyers if the breed you sell is claimed to lay "rainbow colors of eggs, from blue to green to even pink!"
Really it is all about productivity and hardiness - I bet their Wyandottes look nothing like show-qaulity Wyandottes because they simply lay better. And hatcheries need a better egg layer for a big demand. Plus, breeding Araucanas to look true takes some study with the tufted and rumpless genes - And I don't think they had the time or people for that, so they just mixed them, who knows. . . Sadly I doubt asking a hatchery why would ever get an answer. I'd love to try and ask though - The whole Araucana/Ameraucana = EE thing is on my mind all the time.