Yes, very misleading even if 'technically' correct.
Presumably the problem comes because in the lesser populated but larger geographic areas a small community's outbreak is then shown across the authority's domain. If this smaller community is a low number it is also then, presumably, factored up to the 'cases per million' such that if five cases were identified in a community of, say, 1000 people this would be represented by the 5000 cases pm. colour.
For the map to be truly representative the algorithm would need to factor in densities of population and rationalise the community area boundaries to a level playing field of similar sized samples.
I would assume though that this is being done and that the map shown is just one of many representations prepared for the authorities to understand the problem as this next phase is developing.