Still doesn't sound like a high enough concentration of mercaptan to me. Mercaptan levels in natgas are extremely small (odor detection levels at the human nose are around 1 ppb). I work in the natgas industry and have experience with mercaptan.
I also know that natural gas is lighter than air at sea level and would not "settle to the ground" (just FYI)
And I'm a retired Maintenance Mechanic/boiler operator, with a strong HVAC back ground :>} Several more possibilities even based on what you said about Mercaptan. Air handlers {for ventilation, A/C./ heat etc} are many times located on the roofs in many buildings. The article states buildings were evacuated. Makes sense. The air handlers and the elevator shafts would suck the smell right into the building. But boilers are basement dwellers the exhaust stacks however are on the roof usually. I'd check the building and nearby buildings with the biggest complaints.
One building I worked in the gas regulator went bad and would periodically blow off gas. No serious threat but precautions were taken. The valve was far enough away from the intakes it didn't suck in the Mercaptan. One other possibility too is an acid used to flush drains with. The name of it escapes me right now but it can only be used on single level buildings. Just one bottle about 16 ounces can stink up a building big time. It may not even be allowed now I'm not sure on that one.