Uneven background subtraction: Rolling ball vs Disk tophat
I guess the basic question here becomes - what difference does non-flat structuring elements make w.r.t flat structuring elements ?

From the definition of dilation one can see that the structuring element can define a support (like in flat structuring elements) or another function itself (gray scale structuring elements). Look at wiki which defines the dilation operations. The grayscale or numerical version performs a Minkowski Sum. The dilation operation here basically looks for the max on the sum of the two functions. With grayscale dimension one is basically looking at the topographical features of the image level. Its called the rolling ball algorithm since it shaves off non smooth parts of the image which are less convex that the sphere structuring element one defines. The top hat is non flat and basically removes features in each level set and has no effect on the topographical height directly. It depends on the image and problem how these 2 operations are used. One can also write structuring elements to look for connected maximas or minimas(Jump connection), smooth regions(Smooth Connection) refer.