Hire a cleaning company, dump some bleach.   

A mile-long driveway leads to the home, a 10,000-square-foot stunner made of bleached cedar timbers and native stone.

A simple light bleaching of the asphalt shingles will take the stain out of the roof (before the painting obviously).

Does anyone have a lease addendum that spells out what you have to do different, ie, no feminine hygiene products down the toilet, no bleach, etc and that the tenant will be responsible for damage or repairs?   

Depends on how much - doesn’t sound like a lot so you would want to get a fan installed and air movement in that space and spray some bleach on it.

I was told by the septic people that, for this new septic, neither detergent pods nor bleach should be used, because it can clog the system and harm the bacteria (it's a biological septic system).

I don't see any need to swap over to bulk dispenser.We do provide full jugs (96oz) of Tide and Downy plus bleach and Lysol laundry sanitizer for guests use.

Clean the grout with bleach and a toothbrush. 

nothing takes pee out of carpet because probably not in it but in padding and subfloor, when you do pull up you will see, may be able to pull up a corner to check, I bleach floor underneath first before sealing because of bacteria, then install vinyl without seams or will seep again or waterproof surface,  no pets is not always the solutions as you should see what damage including urine humans of all ages could do, at least with pets easier to collect for damages

I decided to purchase new white duvets that could be bleached if needed and washed in high heat.