I don't know anything about automated litter boxes so I can't help you there. I also use scoopable litter and I've found that the low track litters seem much less dusty. I guess it's because the granules are larger.

Have you tried changing Chloe's diet at all? She may need something for skin allergies or she may need supplements for her skin. Have you heard of Avoderm? Here's the link: Avoderm. Maybe this will help her. Good luck.