I think the article said they did their extrapolations from only 2 genomes. I am sure there are a number of genomes of isolated populations that could indicate a much larger population—the Saami of Finland, the Basques, the bushmen and pygmies, Esquimos, New Guinians, etc. Also, the south east Asian areas, especially islands would have been much larger, given that the water level was several hundred feet lower than today.
Regarding the Hobbits, I recently read an article saying that they were 700,000 years old. Of course in the past 100,000 years until they died out, their island would have been much larger because of sea level.
I recently read an article in Archeology Magazine about finding remains in India that dated to right after Toba. I might be able to locate it and add some information if you are interested.
I think that one consideration to keep in mind is that the pre-Toba human population was very widely dispersed throughout Africa and Asia, at least, and maybe into Europe. There is no reason to think that in some of the societies located east of Toba might not have been quite successful and populous.
And, because the ash cloud went west, they would have not been directly affected by the ashfall. Of course, these societies might have been put under considerable stress by the cold temperatures worldwide in the years after the eruption, but maybe not lethally so.
It is also the case that most human populations east of Toba are mappable to the modern genome and area clearly the results of post Toba migrations starting maybe 50,000 years ago. Who knows what might have happened to the archaic populations the new arrivals might have found there?