While the Ferguson site has access to the Mountain Branch junction and the MMC parking garage, it is disconcertingly close to that wye junction that leads to the Marine Terminal and would serve as an obstacle for any freight traffic that wants to pass between the Marine Terminal and the Mountain Branch. Perhaps more importantly, the Ferguson site is really lacking in connections to downtown (the hill, the rails, the parkway, and two coastlines really isolate it). The few blocks' diversions won't make much of a difference for car drivers, but if you want to maximize the number of people that get there from walking, biking, or the bus, a location with direct access to Congress St or Park Ave would be huge.
I feel like the ideal site would be the Union Station Plaza. This would still be close enough to the MMC garage to provide access while also making it just inconvenient enough as to nudge people who live close enough to have alternatives to driving to use those instead. To future-proof it for eventual passenger access to the Mountain Branch, you could make future considerations for a new track branching off from the Mountain Branch to run north to the new station site (either a very sharp curve south of the jail, or a more gentle curve north or it). I think the near-term solution would probably be just keeping the platforms at PTC and making the shuttle service so good that the two sites can be considered one mega station.