We know there’s such a thing as reality due to the reasons you mention, not truth—that’s just a relation between reality and our beliefs.
“Arrangements of atoms” play a role in the idea that not all “syntactically correct” beliefs actually are meaningful and the last koan asks us to provide some rule to achieve this meaningfulness for all constructible beliefs (in an AI).
We know there’s such a thing as reality due to the reasons you mention, not truth—that’s just a relation between reality and our beliefs.
“Arrangements of atoms” play a role in the idea that not all “syntactically correct” beliefs actually are meaningful and the last koan asks us to provide some rule to achieve this meaningfulness for all constructible beliefs (in an AI).
At least that’s my understanding...