Perhaps you can do it without the third table:

select

coalesce(june.level, july.level) as 'level'

, coalesce(june.sthdi_code, july.sthdi_code) as 'sthdi_code'

, coalesce(june.Functional_Area, july.Functional_Area) as 'Functional_Area'

, coalesce(june.Quantity, 0) as 'Qty_june'

, coalesce(july.Quantity, 0) as 'Qty_july'

, coalesce(july.Quantity, 0) - coalesce(june.Quantity, 0) as 'Difference'

from june

full outer join july

on june.level = july.level

and june.sthdi_code = july.sthdi_code

and june.Functional_Area = july.Functional_Area