While I agree about your statement that Naitoh's own additions expand the lore faithfully, the way Naitoh added them outside of the story and continued the story in a way which ignores them as if they didn't actually happen because they are merely "fan-service" bonus outside of the story has been frustrating me because I don't know how to actually place them into the story since the story ignores them...
Naitoh could easily solve this problem is they actually left a few days of free time between chapters instead of starting each chapter exactly when previous chapter stopped in a way to tell us that everything we did between chapters was meaningless because the story continues exactly when it left off ignoring everything we did between chapters and I don't understand why Naitoh doesn't leave a few days of free time between chapters to continue the story a few days after last chapter in a way to actually include inter-chapters' content into it.