Good catch, thanks for putting up the link.
The fences and gates that block Carroll Avenue underneath the Apparel Center and the Merchandise Mart went up immediately after 9/11 as I recall as a security precaution.
About ten years ago several of us were able to walk Carroll Avenue from Franklin Street east to Lower Michigan Avenue, passing underneath the Quaker Oats and Sun-Times buildings. What I found interesting was railroad crossing signs facing the alleys that led down into Carroll Avenue. A ramp that came down from the river side actually had warning lights also but it had not been used in decades. It had a spooky feeling in the subsurface areas with dim lighting. Doug Kaniuk, if you are reading this post, please submit one or two of your photos from that walk. I know you took a lot of pictures then.
I walked it the first time in the 1980s and you can see my black & white photos from that trip on the Navy Pier line section of this site. I used an Instamatic at the time so the picture quality is not the best but you can still see the remains of other spurs.
I am a little surprised that the writer of the article does not mention that Carroll Avenue continues west of the river also in bits and pieces, though it more resembles an alley.