Hi, welcome to BYC!
Sometimes a little added protein can clear up pasty butt, so I read. Never heard of scaly butt. Sorry for your loss and feel your pain of time spent trying to save chicks. I personally might try adding a little raw apple cider vinager with Mother to the water as it's a probiotic. On top of that I would get some vitamins.. it made a big difference for my shipped chicks. I just got bird vitamins but making sure it has the B's. Poly Vi Sol baby vitamins with NO iron is also a good option.
Can I figure since you say you are not a chick novice.. that your chicks have a place to cool down, not just a place to stay warm? Since that is sometimes the cause of pasty butt?
A lot of breeders still use 16% protein layer feed (it's the cheapest).. which is the bare minimum for egg layers. It doesn't necessarily give enough nutrients to hatch healthy chicks. That is my opinion and many will disagree with me. But for my breeders I use at least 20% and people who show their birds use even higher than that because it gives their birds beautiful, shiny, and healthy looking feathers.
Also, bringing in a clump of dirt/grass helps to build their immuninty before they are put out to pasture full time.
SInce you are still losing chicks I would suggest that you supplement with electrolytes, though it is not *usually recommended to use any supplement for more than 10 days. It's important not to mix stronger than recommended because while vitamins can not be overdosed on, minerals such as potassium and salt very much can. For a chick that seems to be failing I will dose a drop of vitamins straight to their beak. This helped many but not all chicks.
Simple electrolyte recipe is... 2 cups warm water, 2 Tablespoons brown sugar, 1/2 teaspoon
each salt and baking soda. Stir until dissolved and serve full strength. (white sugar is OK but brown is better). Add the vitamins to this solution if you can.
I will also add that even hatching at home, not all will survive.

Sometimes there are things you can't detect and those chicks go in the boxes pretty fast. While MM may hatch all the chicks, the eggs still come from contracted breeders is my understanding. And I don't think big timers care as much about their breeding as some of us do. As long as their birds are OK so are they (my perspective)... But I want the best for my birds and therefor provide the best. Things don't just slip by me...
Hope the rest are well!