1) That's not the CDC. Not even a little bit. You linked to an incubator at Harvard which links to a document produced in response to an executive order and whose suggested citation credits the National Academies of Sciences, a nonprofit, nongovernmental organization. The chain went Barack Obama -> CDC -> Institute of Medicine (a subset of the NAS) -> A committee. At no point did the CDC adopt or endorse this report.

2) Following the trail of sources from the link you provide eventually gets you to https://www.nap.edu/read/18319/chapter/3?term=defen#15 which repeatedly states "the exact number remains disputed" and "is a controversy in the field." The document does not endorse ANY particular figure, and provides 108k, 500k, and 3M as estimates produced by surveys. There is no discussion of the validity or reliability of these surveys in this cursory overview; given that the numbers remain controversial and disputed I expect that both these properties are wanting. All the estimates come from academic sources, not governmental entities.

The CDC did study defensive gun use in the 1990s.

https://www.forbes.com/sites/paulhsieh/2018/04/30/that-time-...

The TL;DR is that we don't have reliable data.