Most people, though—like Julian and his group—were not at all nice to Auggie, especially in the beginning. I don’t think people were even trying to be mean necessarily. I think they were just a little weirded out by his face, is all.

Je tohle použití správné? Mně by tam logicky chybělo “that” nebo tak něco…

Jako druhá věc mi přišel trochu zvláštní slovosled s obratem THAT IS:

But after a couple of months, people did start getting used to him. Not that they were really nice or anything, but at least they stopped being mean. Everyone, that is, except for Julian, who continued to make such a big deal about him! It’s like he couldn’t get over the fact that Auggie looks the way he looks! As if the poor guy could help it, right?

Pokud si vybavuji, tak většinou vídám THAT IS až po předmětu, ke kterému se vztahuje, takže bych možná spíš řekl: “Everyone except for Julian, that is…” I když je fakt, že by se pak hůř napojovala ta vedlejší věta… Takže obě možnosti slovosledu by asi byly v pořádku?

1. You're right. Without “that”, the syntax is faulty (or at least “non-standard”). I think they were just a little weirded out by his face, that is all. Omitting the word “that” may be an AmE dialectical feature. The sentence is still understandable without it.
2. Not that they were really nice or anything, but at least they stopped being mean. Everyone, that is, except for Julian, who … This is ok.

Here's another example: “We spent the weekend at our country cottage and everything was fine. Everything, that is, except for the fact that my daughter picked up several ticks (klíšťata), my son broke his ankle, and my wife lost her wedding ring.”