I am reading Notes of Mathematics for Computer Science(MIT 6.042J). And I'm stuck in the Modular Arithmetic Section which I mark with a RED LINE.
I want to know what is trying to say.
Is it trying to say that $(\operatorname{mod} 7)$ is neither associated with $29$ nor $15$?

This is largely a matter of finding whatever focus helps you to understand the process going on here. The $\pmod 7$ is describing what kind of equivalence ($\equiv$) we're using - so $\pmod 7$ is not "acting on" either of the numbers in reality. To bring the $\equiv$ and the $\pmod 7$ together, you could imagine that the comparator is written as $\color{red}{\underset{\bbox[2px]{\bmod 7}}{\equiv}}$ or even $\color{red}{\underset{\bbox[2px]{7}}{\equiv}}$ with reasonable clarity, if that is a useful way of understanding for you.
So what does $29 \equiv 15 \pmod 7$ (or in the above variant notation $29 \color{red}{\underset{\bbox[2px]7}{\equiv}} 15$) actually mean?