The Big Dig was less than 10 miles, never deeper than roughly 100 ft. TARP is over 100 miles always deeper than 100 ft. And because of intended use, it all has to be dug through solid limestone bedrock. The engineering challenges are non trivial in both, but one is on a massive scale that the other is just not.
Speaking to the Seattle example, the reason for building the streets higher is that, in Seattle, people would have revolted if they had decree'd "All shalt raise thine buildings 12 to 24 feet as did the multitudes in Chicago." That's what I mean. Seattle is the example that proves the rule. No one had the political capital to force a Chicago style raise on Seattle.
That said, between you and me, as an engineer, I would have done things the Seattle way and left the buildings at ground level. Raised the streets and then turn the formerly ground level floors into basements. It's not the end of the world if basements flood from time to time. And some drainage might even help with that. Chicago, on the other hand, wanted the "complete" solution. They were done with dealing with floods. Even in basements, they were intent on eradicating flooding. Which is a laudable goal, and Chicago has been much better off because of it. But the risk and the cost is just a whole lot higher than I would have felt comfortable with given the tech available to me at the time.