> Most of the ways to get to Queens, Brooklyn or Staten Island by car won’t be affected — same for the Bronx obviously.

That's incorrect. All of the bridges and tunnels other than GW and Randall's Island (RFK) enter or exit from this new zone. With this new plan, literally all of the ways to get to Manhattan by vehicle will now have a toll. Some will have two.

I suppose if you're willing to take the tiny bridges from the Bronx into Harlem you can still get around tolls, but good luck with that.