Where an authorization or permit is required from the City Planning Commission pursuant to this Chapter and where a permit is required from the Departments of Transportation or Buildings for land contour work, by the Department of Environmental Protection for storm water drainage systems for buildings or adjacent areas or where construction of a public improvement project is undertaken by a City agency, the Department of City Planning and the agencies involved shall jointly determine the conditions under which such proposed development, enlargement or site alteration within a Special Natural Area District will best meet the purposes of the Special District. Applications for any required permit or authorizations shall be filed simultaneously with each agency requiring a permit.