There's no indication that Microsoft themselves keeps track of which individuals downloaded/installed which programs.
The issue this article seems to propose is that somebody could sniff the network traffic between yourself and Microsoft to grab the SmartScreen data and see what you'd installed when Windows contacts MS to see if the file is marked as safe/unsafe/unknown.
If they're in a position to do that, wouldn't they theoretically be in a position to have potentially snooped on the download of the software which is triggering the SmartScreen traffic? (Depending of course, on where in the network their sniffer is at.)
The only valid complaint seems to be that Microsoft is using a known-insecure version of SSL for the website all this data is sent to. If they fix that, I'm not sure what reasonable issue would be there.
I would argue that for the average user, SmartScreen is a useful feature and having it turned on by default (assuming MS is tracking individual user downloads of software for some nefarious purpose) is a good thing.