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Yes there would be multiple stages of action seen within a single sample due to the size of microbiology.

I believe that elements of terrain theory are demonstrated within germ theory, as in immune compromise and opportunistic infection, all infection can be see as opportunistic, but I don't see there being the generation of pathogens from benign microbes due to the presence of diseased tissue. The microbial nature doesn't change, just the body's ability to regulate it. So in times of dysfunction, infectious pathogens become overpopulated and cause symptoms. You can see that with candida where it exists naturally on our skin but becomes a yeast infection when overgrown.