Well, the results differ in their dimension. One is a nxn-matrix, the other is a dxd-matrix. I don't know the application for nxn-result, but when I used the covariance matrix to denote the variation of a vector in R^d (with measurements X = [x1,..,xn]) the result has to be a dxd-matrix, whose eigenvectors and -values indicate the main axes and extends of an "variance ellipsoid" (which must be given in dxd)
PS: Only half an answer, I know
Addendum: Kernels are used for creating inner products of pairwise features, thus reducing the dimension to 1 to find patterns more easily. Have a look at http://en.wikipedia.org/wiki/Kernel_principal_component_analysis#Introduction_of_the_Kernel_to_PCA to get an impression, what the kernel covariance matrix is used for