The best reason I saw for not tunneling under the river, was that they want a station close to memorial on the north side of the river, and the tunnel would be too deep there. I assume they think will be a foot traffic friendly area.
I hadn't really looked at the down town alignment yet. You'd think it would have made more sense to give the train its own bridge and steer it towards 2nd further north.
I'm sure there is a reason they haven't considered just building another bridge right beside center, I wonder why?