The diesel modders don't have to tolerate the smoke. It's behind them, and the impression I get is that they don't care if others tolerate it or not. New diesels are harder to modify, and the cost of a new DPF likely will have them stopping on daily drivers.
A long expansion stroke is also why a premium gasoline, Atkinsoned, and direct injected engine are more efficient. Diesels get a further efficiency boost by not having a throttle plate. When a throttle plate is partially open, the engine has to suck harder to draw in air. That and other associated affects are referred to as pumping losses. Diesels control fuel flow instead of air flow to control engine speed. So they don't need a throttle plate that even wide open restricts air flow to a degree. It's the difference between using a narrow and wide straw with a shake.
The lack of throttle lets all the air in that the diesel needs burn. At idle and low demands means that there is more oxygen than needed to burn all the fuel in the cylinder, or less fuel to burn all the O2, thus why it is known as running lean. This great from an efficiency stand point. You don't risk as much fuel not getting burnt due to a lack of oxygen. The Civic VX and other fuel misers of the past used lean burn with gasoline for this reason.
The reason gasoline cars no longer do this is because of the formation of NOx from the unburnt air. Gasoline engines' throttle plate actually helps here. The ECM controls the amount of fresh air entering the cylinder so that there is just enough oxygen to burn the amount of fuel being injected. Diesels now have an EGR system that helps in controlling the available oxygen, but can only do so much.
Now that there is ULSD available, a three way catalytic converter can now be used with diesels. Previously, the sulfur would poison the catalyst for NOx reduction. They still produce more NOx than gasoline engine before the cat though. A NOx trap is one solution. These bound up the NOx during times, such as idling, when more is produced, and then slowly releases it so that the cat handle it.
The other way is to use SCR(selective catalyst reduction). This is the system that uses urea solutions such as AdBlue. Generically, they are known as DEF(diesel exhaust fluid). It adds to operating costs, but is quite low for the benefits. As long as you don't buy it from a Merecedes dealer.
The plus with SCR is that it doesn't reduce fuel efficiency like an EGR alone or NOx trap can. Compare the TDI Jetta and Passat from a couple years ago. The Jetta didn't have SCR then and the Passat did. Despite being larger and heavier, the Passat has nearly identical EPA ratings to the Jetta. Nearly all new passenger diesel vehicles in the US are using SCR.