App Store ignoring System Pref. settings

Today I awoke to an App Store notification that there were updates available.  I was given two choices, 1) Install 2) Later (with some options).  I opened App Store app to see what updates were supposedly available and there was the one update I was putting off which was XCode.  I didn't want to install it now.  I knew that I had changed the App Store settings in System Preferences to olny check for updates but not act on them or download them so I opened System Prefs. and verified this.  Sure enough, I had only one item checked (Automatically check for updates).  Everything else was unchecked.
So, I have a few quesstions;
Why is App Store ignoring its own settings and download an app I didn't want yet?
Why did the notification only offer me two options (again ignoring its own settings)?
Why didn't the notification tell me which updates were available?
And some comments;
This is just an unacceptable way to approach updates, IMHO.  I need control over what is going to be downloaded and when (bandwidth control and timing).  I must know what is ready for update beforehand so I can understand what it means and be able to opt out or delay it to a point when I am ready (control over what is going to be updated vs what is not and when).
--Carl-

First, open Disk Utility, select your hard disk, go to Partition and create a volume. Move your files to it. Then, press Command and R keys in boot, open Disk Utility, erase the Mac volume and reinstall. When the install ends, transfer your files to your account and delete the volume

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