I was just starting to think this through myself.
Figuring out which parking facilities (or other buildings) are included in the plan is not easy. I had originally assumed it was the little used lots by the river on the other side of the 87, but when I reread the following in the NY Times article, I start to wonder (emphasis added).
The developers say they have a binding agreement to buy the GAL Manufacturing factory on East 153rd Street, near the Major Deegan Expressway. The developers, in turn, would lease the land to New York City F.C. to build the stadium, with the rent subsidizing development of the housing.
The developer is also looking to relocate GAL nearby so the borough does not lose several hundred blue-collar jobs.
For the housing, the developer also has a tentative agreement to buy or lease a large parking garage across the street from GAL and several other parking lots on River Avenue owned by Bronx Parking Development Company, a money-losing company controlled by the city and a group of lenders.
Under an agreement with the Yankees, the city, through Bronx Parking, was required to provide 9,500 parking spaces for baseball games. But a new Metro-North rail station nearby undercut the need for all those parking spaces.
As part of a deal for the soccer stadium, the Yankees would agree to reduce the required number of parking spaces to 6,500, enabling Bronx Parking to sell or lease the land to the developer.
The NY Times also says the development would be:
a 20-acre, multibillion-dollar development stretching along East 153rd Street and River Avenue, between Yankee Stadium and the Bronx Terminal Market
Looking at Mark's map, there are 3 smaller garages across River Avenue from the GAL/153rd site. As you note, those might be included too. And there could be other buildings on the far side of River Ave in the mix. Maybe Rupert as well. I think the only thing not affected would be the old Yankee Stadium site for reasons well discussed here.