Minor nitpick, but tailpipes aren't the primary source of emissions. The study is about PM2.5[0]. which will chiefly be tires and brake pads. Modern gasoline engines are relatively clean, outside of CO2, though diesel engines spit out a bunch of bad stuff.
EVs do also have higher torque, so that may increase tire-based particles, but you're right that it avoids the brake pads for the most part.
Fewer cars in general is the win from congestion pricing, though.
And lower VMTs (vehicle miles traveled) is also a win for the planet, it's probably the best weapon the average person has access to in the fight against climate change. Transit usage begets transit usage; more fares paid to the agency enables better frequencies and more routes, leading to more people opting to take transit instead of driving... In a well-run system, it's a positive feedback loop (and the inverse, where people stop taking transit, can also lead to a death spiral, as happened across America in the mid-20th century).