Nathen,  I've seen that before.  Lots of variables when it comes to Kitchen cabinets.

Standard heights for kitchen cabinets is 36"
When I first started working at a production cabinet shop, the  cabinets were built 35 1/4" high, 
with a 3/4 counter top would come to 36"  Standard counter tops had an 1 1/2" front edge that hung down 3/4" over the face of the cabinets.  The drawer fronts were an 1" down from the top of the cabinets to allow for the front edge of the counter top.

Now days (at least all of the manufactured cabinets I have used) the cabinets are built 34 1/2" -34 5/8" high. (seen both)
The drawer fronts only hang down about 1/4" - 3/8" from the top.  Normally a 5/8" sub top and the the 3/4" stone will bring the full height to 36" and the built up edge will only over hang the cabinet by 1/8"
 
In the below picture you can see the drawer fronts only down 1/4"


Another reason for sub tops is when there is going to be an overhang to sit at.  
No stone person here would let their stone overhang 12" without support underneath.

Of course these are basic standards,  there's exceptions to, or reasons for,  everything.


Figuring out how to do something you have never done is what makes a good challenge.