Yes, I saw that one when you mentioned it earlier. Very impressive result!
Still, as long as numerical accuracy is conserved, I just don't see, mathematically, how the difference arises. 9 times 10 seconds of average stacked sky backgrounds are equivalent to 9 individual measurements average binned. That being said, "numerical accuracy being preserved" is one of the issues with different stackers.
The fly in the ointment is noise.
Here's a quick OOM calculation to show the problem.
Assume the average sky background is 900 counts and the object is 10 times fainter than the sky, so 990 counts come from object+sky. One sigma noise in the sky (assuming ideal statristics) is then sqrt(900)=30. (That's why I chose 900: to make the numbers simpler.) The noise in object+sky is then sqrt(990) = 31.5. Now subtract the average sky background to find a point source containing 90 counts. However, in subtraction the noise adds in quadrature. sqrt (30*30 +31.5*31.5) = sqrt (1890) = 43.5. As the signal is 90 counts, the SNR is 90/43.5 = 2.1. An object in an image like that is barely detectable --- even with the aid of extreme contrast enhancement, a good catalogue, and the eye of faith. It certainly isn't measurable photometrically.
Now add 100 subs. The sky background now contributes 900*100 = 90000 counts with noise of 300 and the sky + object comes to 99000 with noise 315. The noise in the combined measurement is 435. Now the object contributes 9000 (i.e. 90 * 100) counts and the SNR is now 9000/435 = 21. That is very easily measurable and will give a precision of about 0.05 magnitudes.
TL;DR. Adding N subs lets you detect and measure objects which are sqrt(N) times fainter. In this sentence, the important word is measure.
(Thinking about my earlier post: the sky brightness could well have been significantly brighter than the 21.0 m/arcsec^2 assumed. Jupiter was close to the FOV and scattered light from the planet is readily visible in the image. If this was the case, Praxidike may have ten times or more fainter than the sky.)