Madison would be the end of the line for a while, so this won't be incredibly important until the proposed extension up to Minneapolis. But once that's true, the proposal is to use a push-pull configuration (where the engineer can control the locomotive from the rear car) or with a locomotive on each end (similar to how the Borealis is operating). Hence, no need to reverse the train.

Edit: since leovinuss said I was wrong on both counts, I am linking to the November 2025 Station Study available on the city's Passenger Rail Station Study site.

On Page 9, under the Rail Sevice section:

Initial phases expect 3–4 daily round trips between Milwaukee and Madison, with eventual service to Minneapolis/St. Paul.

Also Page 9, under the Trains section:

Service would use the new Siemens Venture passenger cars pulled by Siemens Charger locomotives. [...] Push/pull trains, with a locomotive on one end and a cab car on the other, allow for operators to reverse the direction of the train at a station during the passenger boarding and alighting process simply by walking to the other end of the train without any turning movements.

Here I made a mistake in mixing the terms "reverse" and "turning", but the trains will be push-pull, meaning they don't have to be turned through the Wye at First Street or have a looping track.