I am by no means an expert on the tunnel, but yes the impetus behind the project was to remove land from the Waller Creek Floodplain.
However, I think, that this close to Town Lake the flooding from the Lake itself might impact the site. We would have to know the lowest adjacent elevations and compare them to how far up the floodplain from the Lake would go.
At this point, all we can do is speculate until the site plan is submitted.