Very interesting article highlighting a lot of hard facts, but also a lot of conjecture in my eyes. Speaking from experience with feral cat populations, I was heavily involved in TNR in Greece for a number of years, particularly on islands in the Cyclades where things can be dire.
We found that the worst thing to hit cats was invariably conjunctivitis, FIV and cat flu. In terms of population I'd say we were dealing with several hundred to 1000 at any given year, a number that remained steady as many cats didn't survive long. 
We never found any outbreaks of toxoplasmosis or rabies but we were a coordinated and conscientious team. 
The points raised certainly are valid but also highly dependent on location I feel. Truth is one female can be responsible for upto 20000 births if population is left unchecked by neutering so take from that what you will.