likely not, most of the buildings you mention were torn down or burned in 1871. There only a few areas in the city where these buildings still exist and they are small single/multi family building that will stand until somebody decides to knock them down. Most of the buildings in question are the sky scrapers which were first built in 1885, the streets were raised in 1855.

It's still built on marsh/mud

Are there not pylons down into bedrock below the marsh and mud?

The John Hancock building has some of the deepest caissons of any building in the world into bedrock.

Yes, but that bedrock is way down there.

From [0] : “Construction of the John Hancock Center began in 1965; however, was stopped in 1967 because the building kept sinking. Because of the John Hancock Center's lakeside location, 57 concrete caissons had to be sunk into 10 ft wide holes drilled 197-feet below grade into bedrock, resulting in the John Hancock Center having the deepest foundation of any building at the time.”

[0] - https://www.beck-technology.com/blog/how-did-they-build-that...

In many places foundations are not sunk to bedrock, rock is far too deep to reach. Instead the pilings use friction to maintain their position.

What places besides the mess in SF ? (I'm not sure how to search such a query, but super interesting)

Bedrock is very deep in Seattle. You can see the map here: https://pubs.usgs.gov/mf/1692/plate-1.pdf

For instance the space needle is just on a giant hunk of concrete that is only 30ft deep. https://www.spaceneedle.com/history#:~:text=An%20underground....

But from memory most large buildings in the downtown area are on deep foundations in soils, not to bedrock.

Are you thinking it might be decay heat from the marsh? With the right conditions, compost heaps and peat bogs can light themselves on fire.

I'm just thinking the journalism sucked to not even mention any of these obviously confounding factors.

Chicago's foundations are inherently unstable. IMO it makes being scientific about blaming "underground climate change" substantially more difficult. The journalist is out to lunch after strictly reporting on what these specific folks are saying and measuring.

If I didn't live and work there for years in the distant past, having spent many a nights drinking in bars below grade because of its history, I wouldn't know the amount of speculation the "science" reported in TFA really calls for.