Wish I could magically answer this for you. When treating Dirtbike, our vet did prescribe prednisone, even though it's contra-indicated for pts. w/fungal infections.
I figured it this way:
Dirtbike was going to die. I had to triage her systems, and breathing came first if I wanted to keep her heart going, so I used prednisone to reduce the inflammation and keep her going. I cranked up the fan, read to her, talked, petted her, and just hoped.
When she was not in crisis, I didn't give it to her. I did use pseudo-ephedrine in very small doses, I loaded her in the car, put her head out the window, and drove.
But the prednisone I only used for emergencies. She was in this shape for a couple of weeks, maybe more, and it was exhausting.
I can't tell you that your vet is right or wrong; they went to school and I didn't.
I think it depends on your animal and what it takes to care for him at the moment. For us it was sometimes minute by minute.
Here are some links and excerpts about prednisone, but they don't say "WHY". I'll do some more searching, and maybe come up with the why, but here's this for now. Hope it helps-
Precautions and Side Effects:
While generally safe and effective when prescribed by a veterinarian, prednisone can cause side effects in some animals.
Prednisone should not be used in animals with known hypersensitivity or allergy to the drug.
Prednisone should be avoided in fungal infections.
Prednisone should not be used in pregnant animals, since it can induce labor.
Extreme care must be taken when stopping prednisone therapy. If an animal has been on prednisone for an extended period of time, slow weaning off the drug is critical to avoid serious complications.
Prednisone may interact with other medications. Consult with your veterinarian to determine if other drugs your pet is receiving could interact with prednisone. Such drugs include non-steroidal anti-inflammatories.
Adverse effects include increased thirst and appetite, panting, vomiting, restlessness and diarrhea.
Some animals may develop stomach ulcers from prednisone use.
Long-term use of prednisone may result in loss of hair coat, weakening of the muscles, liver impairment and behavioral changes.http://www.epler.com/IPFWhat'sIPFTreatmentOptions1.htm
"Prednisone also decreases the immune defenses to certain types of fungal infections and atypical bacterial agents. It is important to obtain the list of adverse effects, review them, and monitor them."