I don’t think the study takes into account any genetic testing or factors, and those would weight the decision one way or the other. But what the summary does imply is that they are comparing apples to apples. They found extra cancer in 1-3% of the amputated breasts. That is probably what one would expect to find in a ramdom sample of amputated breasts. The study shows that amputation has no effect in most cases (probably all except the ones with genetic predisposition).
There’s more to the study and the JAMA article. The Daily Mail article is putting out half the story and not making the information clear enough. Plus, there are many, many other factors - such as cancer stage, placement of tumor, number of tumors, pathology, genetics, etc. - that sometimes necessitate a single or double removal. As for finding cancer in 1-3% of the “healthy” tissue removed, the whole point of having prophylactic surgery is to have it removed before cancer develops. So, there shouldn’t be cancer on the healthy side at all.