Git - definition of commit from the booklet "git from bottom to top"

I read "Git from bottom to top" and defines "commit" as follows:

"The end is a snapshot of the working tree at some point in time"

However, I do not agree with this definition. You can have 5 files (1 new and 4 changed) in the working tree, but only 3 are added to the index. Therefore, if you commit, your commit will not match the current working tree.

Is there something that I am missing, or am I right?

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