I was a bit concerned that the first floor staircase was not visible and intrigued that the staircase on the left uses the same components as the original building, though while not shown on original maps, it does appear on the 1903 Motor show map.
The semi-circular structure on the first floor, left-hand side of the image, does match the shape of the Grand Orchestra.
I have often wondered what survived of the sculpture courts, an illustration on page 209 of the "Musical Life of the Crystal Palace" shows the cigar shape of the opening of the Grand Orchestra, extending far into the nave either side.
The staircase is definitely there in later plans like you say, just not in early plans/pictures, and Ken Kiss already confirmed the colour photo is taken towards the side of the organ in the northwest central transept area, but the problem I'm realising is altogether different...
Are we being deceived by your plan of the Centre Transept; the one that is based on the floors above? Could there be enough room in-between the Egyptian Court and Organ to fit two open rectangular spaces? Rather than depicting the same area, could the two photos instead be depicting (2) different adjacent areas in the northwest centre transept?