Zones I, II and III of the Aquifer Protection District shall be considered as overlaying all other zoning districts within the Village of Endicott. Any uses permitted in the districts so overlaid shall be permitted only subject to the provisions set forth in this section. Nothing contained in the Aquifer Protection District regulations shall be construed to reduce or amend provisions contained in Chapter 250, Zoning, of the Code of the Village of Endicott.