In the study researchers were focusing on brain cells. The brain generally has a high rate of blood flow so by your reasoning brains cells would be less affected than low-flow regions like the eye. But measurements would have to be taken at a specific site to know for sure, in this case that would be in the intracranial space.

The RF was probably too low power to produce readily measurable effects on temperature in the brain. I imagine that it could be a difficult piece of data to collect. However, you're undoubtedly correct that whole body temperature wouldn't be informative in such a study.

Makes sense, keeping some distance from running microwave ovens is a good policy. After an oven has been in service for some time what are the odds seals become leaky, etc. Probably not a great risk but no harm in minimizing one's exposure.