Why do some Parmigiano Reggiano contain bacterial cultures? I was under the impression from what I have read/DOP specification that only rennet was to be used for Parmigiano Reggiano.

Milk coagulation, obtained exclusively by the use of calf rennet, takes place in bell-shaped copper vats; up to two wheels are made for each vat.

Yet, I come across many Parmigiano Reggiano cheeses imported from Italy with the real Reggiano logo and the DOP symbol (e.g. Tre Stelle, Italissima, President's Choice, Compliments, etc.)

Is it just a loophole in the specification and found only in lower-end Parmasen Reggiano?
The bacterial cultures are what the document you quoted from refers to as "fermented whey".  The previous paragraph in the Specification of the Parmigiano Reggiano Cheese from the Parmigiano-Reggiano Cheese Consortium 
 web site reads as follows:


  Fermented whey is added to the milk, which is a natural culture of lactic ferments obtained from
  spontaneous acidification of the whey remaining from the cheese-making process of the previous
  day.


All Paramgiano Reggiano cheeses would have these bacterial cultures in them, not just the cheap ones.