Fermentation is a term that is used fairly loosely in the general cigar vernacular. Biochemically, the definition is quite a bit more precise. The third "fermentation" that only Cohiba undergoes (at least among Habanos) is not really a fermentation per se. It's more of an "aging" in barrels.
A quick google turns up a whole host of links but the key fact to keep in mind is that a genuine fermentation requires microbial or enzymatic action to chemically convert one class of compounds (carbohydrates such as starchs and sugars) into another class of compounds (acids, alcohols, etc.) Additionally, this reaction generates heat*. In tobacco, the action is bacterial and anaerobic. Even more specifically, in tobacco, the conversion of interest involves nicotine and other alkyloids being transformed into pyridine class compounds. Pyridines and ammonia share common conversion pathways so that is why tobacco fermentation is an ammonia-generating fermentation whereas beer fermentation is not.
Wilkey
*The CA link makes it sound like the mass of the pilon or bulk is what makes heat. This is incorrect.