Q: If 3 tracks are to be used for commuter rail, should it be assumed that those tracks may be in the current terminal-type configuration?

No. Please use the reconfigured track arrangement per the drawing file named:

Competition Plan_Concourse Level_Track

This file is enclosed in the .zip file named "Drawing Files" on the Competition Downloads section of the Competition site.

NOTE:
Based on our conversations with rail planners in Chicago, this competition assumes a massive re-organization of rail--both high-speed intercity and commuter--that would likely result in a redistribution of commuter lines among the four existing downtown rail stations: Union Station, Ogilvie Transportation Center, Millennium Station, and La Salle Street Station.

You should assume that the Concourse Level Track Plan is sufficient for the Intercity High Speed Rail and redistributed Commuter Rail loads.

In short: please use the provided drawing. As noted in the brief, this competition is about much more than the resolution of an element of infrastructure, and this is why we have provided you with a common plan for rail organization.