Ubuntu's software updater is not GNOME Software! GNOME Software does not listen to Ubuntu's software updater settings. I know this because I've got Ubuntu's updater set to run every other week, but I keep getting updates daily.
I found this on the Ubuntu forums, there is an edit on the original post with the solution to both problems. Use dconf-editor (may need to install), go to org.gnome.software, and uncheck "download-updates". GNOME Software should no longer check for updates, and Ubuntu's Updater should continue to update as usual. I'm not entirely sure, but I'm willing to bet you will need to log out and log back in for the change to take effect.