>>12520821The only reason why I can see the recent chapter coming off as dark is because of everyone's fear of the door.
The reasoning behind that, is that doors in Equestria are soft and inviting, while doors on Earth are harsh, repelling, and concealing.
Anon ponders this at one point in the first two chapters. It's a throwback to that.Anon never bothered to investigate the tower until now because of the door. Since he recognized his feelings of that door's presence being similar to his feelings of doors on Earth, he never bothered with it.
The only reason why he chooses to now is because Speck disappeared in the middle of the night and was gone a while. He assumed that something could have happened with her and the tower. He goes to investigate and coincidentally runs into her and Luna. Speck just so happened to have walked to that garden.
Luna and Celestia never bothered with it, because of their similar fears of the door, and because it never posted an imminent threat.
The tower was an imposing structure in the middle of a garden. It was jarring in and of itself. It scared Speck, which prompted Anon to actually put thought and effort into doing something about it. If the tower really did contain something that could cause harm to Speck, he wanted it gone at any cost, even his own life.
He took the books instead of any of his other things, mainly because most of his things would be too out of place in Equestria. The books and their stories are something he wants to share with Speck. Anything else would take him back to his memories of Earth and he and Speck have repeatedly mentioned that it's time to let go of old memories and create new ones.
He can get enough of his old memories from the presence of the books, but he can also share some of his favorite adventures with someone he loves, while the both of them create new memories from it.
tl;dr: You're reading too much into the large details and not enough into the subtle stuff.