They're not interconnected, saves of Act 1 won't work with Act 2, but it continues the story.Why is the game in three files? How does that work for game progression between chapters?
He simply split it to make it easier to deal with, so that the game doesn't get too big file size wise.
As for the Renpy, think of it more of a side story, doesn't connect with the main one, but nice to play through