Steroid myopathy is not unusual with prednisone. Atrophy is really a different condition and is usually associated with disuse of the muscles causing them to shrink and weaken. Myopathy is an inflammatory process that weakens the muscles.
Steroid myopathy can often be reversed when stopping the meds but not always after long term use.
I would suggest that you get a second opinion from an experienced rheumy.
MCTD (lupus, scleroderma, polymyositis). Diagnosed 2005. Kidney, liver, GI tract, dysphagia, raynauds, Barretts esophagus, quadriplegic in 2005. Recovered and now active in skiing, tai, chi, hiking, golf. Meds: prednisone 2.5mg, imuran 25mg, amlodipine, benazapril, omeprazole, potassium, folic acid, vitamins, maxide and various supplements and vitamins.
Remain optimistic and you can overcome the odds.