It mentions in that spreadsheet that the $0.004 the artist gets per stream is minus the 9% that CDBaby takes off the top. So, it's really like CDBaby gets $0.0045 per stream, and they give 90% of that to the artist.
It occurs to me now, though, that I've read in the past that Spotify doesn't actually pay the same amount per stream to every artist or label. Apparently it doesn't even pay the same amount to the same artist each quarter.