As cells are discharged, their voltage drops. If you have two cells in parallel and one of them 'uses up the chemicals first', then its output voltage will drop, and the other cell will start carrying the load current. The net result is that you can't have one cell discharge to a lower voltage than the other.
I suppose that if a particular chemistry had the characteristic that the cell fails as a short circuit when it is drained, then two cells in parallel would have the issue that one could discharge and short, and the other one would still have capacity, but I don't believe that this would be an issue with any chemistry if both cells had the same capacity at the start, since both cells would discharge at pretty much the same time.
-Jon