Some cases of the Black Death did not fit the symptoms of bubonic plague.
Look also at the disease vector. Plague is endemic in the marmot population of central Asia. In the 1200s the Mongols were on the move, the Silk Road got disrupted, and people travelled heavily in marmot territory (note that the plague is now endemic in prairie dog populations in our own Southwest).
Caravans and merchant ships took plague (in rats) to port cities all over Europe. The paths have been tracked. Animals were constantly close to people, and people had poor hygiene. Fleas got around. Rats were one way, but you didn't need rats. Fleas can travel on horses and in clothing.
Plague is very well studied -- the Black Death was a huge historical phenomenon.
This new theory seems to imply that travelers from Darkest Africa were coming to Europe in 1348. Pretty sure there is no evidence for this. We know where the reservoir for Ebola is -- basically Zaire and neighboring countries. That was a bit "out of the way" at the time. By contrast, we know that the Silk Road was heavily traveled, and we know it veered into marmot territory.
I don't see this theory having anything to back it up.
I’ve read a number of articles citing evidence that the black death started out as bubonic plague but spread so widely and quickly because it became airborne (pneumonic plague) which is caused by the same bacteria but is far more virulent and kills its victims in a different manner.
Bubonic plague has three different forms, each more rapidly fatal than the previous. Bubonic with the swollen bubos of the lymph glands that turn black; septecimic which is like general blood poisoning and more rapidly fatal, and pneumonic which is spread through the air and highly fatal. Probably the kind of cases that did not fit the rule.
Plagues are not mutually exclusive.
The middle ages also had a plague, mostly in England, called “The Dreaded Sweat”, that killed within a day of the first symptoms, and killed many thousands. Suspicions are that it was similar to hantavirus pulmonary syndrome (HPS), caused by rodent droppings. This also may have decimated the Chinese military during the Korean War.
http://www.historytoday.com/blog/2014/05/dreaded-sweat-other-medieval-epidemic
During that period they also suffered terribly from Dysentery, aka “The Bloody Flux”, Ergotism from contaminated grain, and several other diseases.
http://www.labelle.org/top_diseases.html