I don't know for sure either since I still own GTX 580s which aren't even GPU Boost 1.0 cards much less GPU Boost 3.0 cards.  I do own a GPU Boosted (hacked) GTX 680M in my laptop, so I sort of have an idea of how it works.
 
Below is my interpretation.  It appears that my guess of "about 30 mV" wasn't completely accurate.  It looks like the primary card needs about 43 mV more at base clock frequency.
 
This is an approximation based on an approximation.  The graph is just approximated points and therefore the numbers below aren't 100% correct but hopefully illustrate the difference between the two.  I don't even know if I am reading all the points of the graph properly (blue bars versus yellow line), but at least it should illustrate the difference between the two.  If nothing else, it should show the correct proportion of difference or ratio between the two even if the actual numbers are not trustworthy.
 
My conclusion is that the primary card needs approximately 31 to 43 mV more than the secondary card to maintain just plain base clock frequency, boosts up to max of about 27 MHz less than the secondary card, and reaches max reliability voltage about 6 mV sooner than the secondary card.  Assuming that these estimates are true or at least in line with reality, I would conclude that the new card you received just happens to not be as high up on the silicon lottery winner's list.
 

http://img.techpowerup.org/161014/6th91qt.png
 
 
These are the calculations I used based on approximations shown on the graphs (assuming that the graphs are accurate and assuming that I am reading the graphs correctly):
 
 
Min base voltage of primary card:
491 pixel postion - 247 pixel postion = 244 pixels
1162 mV - 881 mV = 281 mV spread
281 mV / 244 pixels = 1.15 mV per pixel
257 pixel postion - 247 pixel position = 10 pixels
10 pixels * 1.15 mV per pixel = 11.5 mV more than 881 mV = 893 mV

Min base voltage of secondary card:
No further calculation needed because it lines up with the graph.
850 mV

Min base voltage difference:
Primary card needs 43 mV more than secondary card at minimum boost.

Max boost voltage of primary card:
499 pixel postion - 491 pixel position = 8 pixels
8 pixels * 1.15 mV per pixel = 9.2 mV more than 1162 mV = 1171 mV

Max boost voltage of secondary card:
1243 pixel position - 978 pixel position = 265 pixels
1162 mV - 850 mV = 312 mV spread
312 mV / 265 pixels = 1.18 mV per pixel
1256 pixel position - 1243 pixel position = 13 pixels
13 pixels * 1.18 mV per pixel = 15.3 mV more than 1162 mV = 1177 mV

Max boost voltage difference:
Secondary card may be allowed to use 6 mV more than primary card at max boost.

Primary card min base frequency:
286 pixel position - 151 pixel position = 135 pixels
2.5 GHz - 1.6 GHz = 900 MHz
900 MHz / 135 pixels = 6.7 MHz per pixel
286 pixel postion - 283 pixel position = 3 pixels
5 pixels * 6.7 MHz per pixel = 20.1 MHz more than 1.6 GHz = 1.62 GHz

Secondard card min base frequency:
Same as primary card.
1.62 GHz

Min base frequency difference:
No difference.

Primary card boost frequency at 1171 mV:
286 pixel position - 239 pixel position = 47 pixels
47 pixels * 6.7 MHz per pixel = 314.9 MHz more than 1.6 GHz = 1.91 GHz

Secondary card boost frequency at 1177 mV:
286 pixel position - 235 pixel position = 51 pixels
51 pixels * 6.7 MHz per pixel = 341.7 MHz more than 1.6 GHz = 1.94 GHz

Boost frequency difference:
Primary card boosts 27 MHz less than secondary card at roughtly the same max default core voltage.