I think the problem was generated by the incorrect cell size, which should be read from the HDF5 file attributes. Anyone has a good idea of how to correct this issue?
according to
Multidimensional raster types—ArcGIS Pro | ArcGIS Desktop
non raster data is ignored... but it isn't clear whether that includes coordinates and/or cell sizes... so it guesses at a cell size, which is probably just a reflection of rows and columns (assuming continuity in space and it doesn't represent sparse data).
I suspect you have to troll the remainder of the data to find out more information to use it as a 'map'
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