forget, the 'quarry' you refer to is, by the looks of it anyway, a remnant of the construction of the two runways, i.e. a depot, a yard where concrete was being made.
If you use Google Maps (not Google Earth), and you zoom out to 1000ft/200m, it appears to be part of a now-rerouted motorway/dual carriageway between the north-west and the south-east end of the airport (zoom out to 1km/1mi ratio, and you can see how that cleared bit merges with the southern end of 36R, and naturally appears to continue to the northern end of 33R).
Perhaps our Spanish/Madrid residents can help out on what changed when MAD T4 was built; there are two crossing points on the southern creek and the northern creek (where the fuselage ended up). But there IS elevation, that much is clear.
I found this link that explains some (but not all) of the changes:
Madrid Barajas International Airport (MAD/LEMD) Airport Technology
S.