Are the exercises in the end of Section 1 and 2 (Master Key) really just meditation?
Yes, essentially. But it is meditation with a purpose.
As with all things in The Master Key System, it is ideal if you can understand the exercise within the context of the entire text of the chapter, and not just one paragraph.
The preamble of the chapter says this:
Most people (including myself) accomplish our thinking process by chaining together an almost constant stream of random thoughts. Some of these thoughts we are scarcely aware of. How valuable are these thoughts, really?
The exercise is meant to help you achieve mental mastery. The purpose of the exercise is to show you how to take control of that stream of thought. By quieting the mind, we learn the ability to replace the random stream of thoughts with new, carefully chosen, more powerful thoughts.