You'll get parasitic C values for any layer that has an area and fringe capacitance defined in the parasitic extraction definitions in the magic techfile. That will include li, poly, and well, as well as inter-layer capacitances between any of those layers and any other, or between themselves. Only transistor gates and source/drain are not extracted as parasitics because they are included in the device model.
As far as the hierarchy: Magic will write the parasitic capacitance for just the cell by itself, and the parasitic capacitance for the parent cell, by itself. Then if there is any redundant overlap, it will add a negative capacitance equal to the amount of overlap to compensate for the duplicate counting of the caps.