I imagine some aspects of building horizontally might not scale as well as vertical construction.

For instance, it looks like the Navy Pier Flyover touches the ground in many different places along its half-mile length, each of those places will have different junk buried there already, unique challenges and access restrictions, and new ownership/usage agreements.

With the skyscraper you dig one messy hole then stack and connect layer after layer of engineered rectangles.

In the mid 19th C Brunel built a ~100 mile long railway line in 5 years, the route was dug out by hand with picks shovels and wheelbarrows. It's a marvel of engineering with a route alignment that would allow trains to travel at well over 100mph. However, over a hundred people were killed just digging one of the tunnels on the route. When the Sears Tower was built there were probably still guys walking along the bare girders with no safety harnesses. So that's probably part of it.

The flyover is free. The sears tower collects rent. If you pay for fast construction with the tower, that means less time not collecting rent which might work out better. If you pay extra to expedite the bike bridge, whats the point? Its a cost center for the city either way. Getting it done faster just wastes the public's money giving them the same thing they would have gotten anyhow.