The quantum fluctuations that occur during inflation do indeed get stretched across the Universe, and later, smaller-scale fluctuations get superimposed atop the older, larger-scale ones. These field fluctuations cause density imperfections in the early Universe, which then lead to the temperature fluctuations we measure in the cosmic microwave background, after all the interactions between dark matter, normal matter, and radiation occur prior to the formation of the first stable, neutral atoms.