Blackwell story line

I recently obtained the Blackwell Bundle and am really enjoying the atmosphere, the voice acting and expressiveness of the characters, achieved despite the low resolution graphics. I have a question about a change in the story line in Blackwell Convergence (3rd game):

It appears to be a minor change in storyline, but I don't know why it was necessary.

I haven't played them but hopefully someone that has will be along shortly with their opinion.

Ana