Hmm not sure I can help but I do have some comments.
The only thing I could find about black spots was;
1. Fish has suffered a chemical burn and is now healing. Check water conditions.
2. A parasitic infection by flatworms called Uvilifer ambloplitis. It requires an immediate host though (like birds) and is only found in ponds.
Neither of these seems to fit your fish.
When a fish suddenly develops identical lesions I immediately assume it has been chased, or frightened, into a space too small for it to fit and it has damaged itself in the attempt to escape. Do you have an ornament it used to fit into easily but is now too big to do so?
I do not know anything about algae treatments but wonder if it is affecting the fish. I have heard of it doing so but do not know what the symptoms are.
Goldfish do not object to current so, unless they are trying to hover as far away from the flow as possible, it won't be stressing them.