It's a little bit different. Makoto's parents indeed get the blessing from the Goddess so they can get accustomed to the new harsh world(compared to the other world). The blessing was supposed to expire.
Her older sister was born when the blessing was still strong, so she got it too. Her...
In the WN, it said the physical young forest onis admire Aqua while the magical young forest onis admire Eris. Shii is the weird case of being on the physical group, but not only she admire Eris, she also tries to copy her personality.
Adding to this, he can "speak" with literally anything. Not only with a language that you can have a conversation with, but also abstract languages, like stone and forest. I mean, how exactly you "speak" with an inanimate object or a concept of collective individuals(trees)? Not even he knows...
Yeah, the cooking competition was a filler, but Alpha reminiscing the early days of Shadow Garden is in the novel. Delta's past is probably also in the novel, I don't really remember.
Interestingly though, there were never a filler before in the manga.
The elf and the dwarf have their own arc in the WN. I haven't read it, I just saw their arc name just like the other girls. Iirc they happened before the last girl(the shortstack bodyguard).