It is a simple matter of the magnetic field surrounding the magnets. If you take the average distance between parts of the magnet, you can easily compare how much magnetic force there is going to be. With the magnets parallel, the middles are only separated by the thickness of the glass, while...
A while back, I purchased a 38W peltier cell on ebay. It wasn't powerful enough, so I'm looking at something along the lines of a 92W. I noticed, however that my 38W and the 92W have the same dimensions and the same number of junctions. Also, dT of the 92W is only 1 degree C above the 38W...