That's a good question, and I could easily see the camera settings (and the light) being a source of error here. Naively, I used the default iPhone camera with the same exposure for each one, then ended up manually removing some of the HDR settings from each one when they were showing up as way overexposed on my computer. Not exactly an advanced, scientific technique, and there was also a bright source of soft white light from the window next to the setup, which could have thrown off the automatic exposure.
Another comment mentioned it, but I wonder if the overall effect would be more visible with yellower baseline oranges (or, as you mention, pale lemons and limes). Really interesting about the LEDs underperforming as well!
Along those lines, one big thing I worried about when reading your article was whether the camera's auto-white-balancing might be throwing everything off. I'm not sure how it works on an iPhone, but I'd suspect that presence of the red bag might cause it to reduce the redness of the rest of the image. One easy solution might be to always have two oranges in each photo---one inside the bag, and one sitting on top.