Even within your views, you cannot deny a cleansing effect from the probiotics.
Nobody really know what exactly happen in the intestines, but if you have a huge intake of food based probiotic, in which the number of organisms is extremely high, so that they do not die that quickly, these bacterias will work to digest toxins in your gut and will try to make the intestines a better place for themselves to reproduce, and since they're of the same type of good guys as our bacterias, they make a better place for these too (pH, etc.).
These food based probiotics (mainly thinking of EM, kefir, sauerkraut, some special home-made yogurt), also contain substances that help these bacterias to establish. Vitamins that are usually produced "in vivo", in our intestines, can be produced beforehand, "in vitro".
I'm against "popping" probiotics too (taking the probiotic pills).