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This is most likely mold as the roof stains are more commonly bacteria. The bacteria in this case like to latch on to rock and stones and thing like that; mold on the other hand, mostly likes more easily chewed material softer material like cellulose, drywall, wood and organic material that sticks to highly electrostatic-charged substances like plastic, hence PVC pipe.
The PVC pipe grabs massive amounts of debris in the air because of its ability to maintain a higher ectrostatic charge and it holds a more constant temperature thought the day/year creating a ton of condensation inside and out. Grab a whiffle ball bat in 110F weather and grab it in -10 degree weather on a sunny day, the teps are not all that much different, but if you grab a metal bat on that hot sunny day you'll burn your hand and conversely in the cold you will again burn your hand, but from the cold.
So that is how the mold gets there but to answer your question: Yes this takes care of that stuff.
Just be careful playing around them because the PVC pipes release harmful sewer gasses and when mixed with almost anything at all they produce a chemical reaction.
You should be fine, just don't get too much spray down the pipe and be all breathing in the pipe and stuff. Sewage has high amounts of ammonia and other fun chems.