I don't think there's a difference here between Science and Mathematics. Scientists also study their tools (e.g. telescopes are studied by Optics), and use the objects of their studies as tools (e.g. galaxies can be used as telescopes, see: https://en.wikipedia.org/wiki/Gravitational_lens).

Edited to add:

The author of the quote tried to find an example that evokes vivid imagery, and also very extreme: it's obviously absurd to confuse a telescope with a galaxy, thinks the layman. While this turns out to be literally false, the point of the quote may still stand. The discipline that studies the real tools of Science is not Science itself, but the Philosophy of Science. This shouldn't be like this, and it wasn't until lately. Philosophy and Science used to be one and the same, but around a hundred years ago they separated, and this hurt both tremendously, in my opinion.