The headquarters of most of the country's large companies are there, but many of them have presence all over the country (like most of the banks). When every year they report their finances to the government, everything gets registered as from their Santo Domingo main office but... It's a technicality that bolsters SD to undermines the rest.
For many years, several commerce companies with stores in the interior too would pass the collected taxes (mostly ITBIS) to the government and while a good chunk was actually collected in stores outside SD, on paper it looked as if everything was collected in SD.