No, no scientific questions remain. The baby is alive and healthy as predicted, with a percentage of abnormal mitochondria too low to cause any manifestation of the disease.
The journal editors are the ones who pointed out the potential issues with the work. So unless you are an expert in the field, you really are not in a position to judge whether or not scientific questions remain. Heck, even if you were an expert, not many people would take such an absolute tone seriously. After all, falsifiability is a basic tenet of the scientific method.
Actually there are scientific questions in regards to life long latent effects that might manifest themselves later on.