Four of the six options are on the east side of the city, which are likely the most practical since they could potentially allow through-running on existing tracks to the Twin Cities that would still mostly follow the existing Amtrak Empire Builder route. Running through on the Madison isthmus would require either continuing west along the Wisconsin River corridor to Prairie du Chien (south of Amtrak's current routing) and north along the Mississippi, or building a connection west of Madison to turn north and rejoin the Canadian Pacific tracks Amtrak uses.
This appears to be a study being led by the City of Madison rather than WisDOT, and it doesn't seem to be tied to any actual plans for new train service. Instead, this looks like it's just to ensure the city has good plans in place if and when a rail service initiative actually happens, such as one using funding from the recent federal infrastructure bill. (Map from the city's site.)
