I've heard of dogs on Blue Buffalo breaking out in hives. The very hysterical owner of one of my pups sold to a pet home called me up at 11:30 pm on a Friday night believing the dog (who was about 6 months at the time) either had a disease or some sort of genetic defect. When I learned she fed BB, case closed, problems solved. Told her to temporarily feed Science Diet Sensitive Skin & Stomach just until her Vet could clear up the situation.
She bought a bag the next morning, took the dog to the Vet that afternoon, and by Monday she had sent me an email with a pic attachment of the dog whose problem had already subsided about 80%. And it originally looked a bit worse than the OP's dog.
Had the same issue with a puppy owner feeding Wellness (WORST.FOOD.EVER.) Both her Beagles developed bald patches with very dark skin underneath, making me suspect both dry skin and yeast infection were at the bottom of the problem. SD once again cleared up the mess, and she still feeds it today.
Problem with those holistic foods is that they are manufactured very much with the dog owner in mind, with little regard to the biological requirements of the dog's eating them. No feeding trials, no research behind the feeds. Lying about the quality and nature of the ingredients and deriding the ingredients of competing brands. Don't know how they get away with it
My advice to the OP - try any formula of Science Diet while the Vet figures out what's going on. This food is miraculous for dogs with coat & skin issues. Regarding fleas, we had a BAD season here. All my dogs were infested like I have never seen before, and they were being cooked for and supplemented with Iams. The pup, however, I had on SD puppy formula, and he was the only dog who wasn't scratching and that I did not find one single flea on. That same pup (my avatar) came to me with a greasy coat, bald splotches above his ears, and generally thin coat. At 4 months, he was not only twice the size the two male littermates his breeder kept back, he also looked like he could bench press them.