Flexibility in the "District" mechanism would not be out of place, historically:
There are oil wells dotting the city of Los Angeles
There are coal tunnels under the cities of Scranton and Wilkes-Barre, PA (some of which occasionally collapse, taking a house or three with them)
Late in WWII, both the Germans and the Japanese dispersed their 'Industrial Zones' among Neighborhoods in their cities to avoid Allied bombing (with mediocre success - in Japan's case, the US simply fire bombed all the cities)
In other words, it would not be out of place too, say, get the benefit of a Resource under a District, but it should require extra work to get it - perhaps a Builder Charge on top of the District and also, most extraction processes being less than ideal neighbors, perhaps a drop in the basic Appeal of the Tile and the neighboring Tiles - which could be a nasty shock to the Housing from your Neighborhoods in the area, but wouldn't make the Resource completely inaccessible.