I think there is some confusion here: The fusion models examined do not predict the fusion from the local configuration of bases. The main evidence for fusion has always been the fact that the two pieces of human chromosome 2 are nearly identical to chromosomes 2A and 2B of apes - typically 96-98% identical. The genes are almost entirely in the same order, the inter-genic regions are very similar All along the 2A/2B length - millions of bases. The site of fusion ad models for its occurrence is merely confirming what we already - there are two chromosomes somehow stuck together. Since both papers focus on the site of combination and do not adequately address this primary piece of information, they seem to be missing this point.
InAs to your last question - I don't know if its necessary that chromosomal fusion must occur in every living thing, but it appears that it has. In fact what we see as we look at all the diverse chromosomes being sequenced, is that most chromosomes have been merged or rearranged over and over again. Over long periods of evolutionary time, a typical chromosome looks like a patchwork quilt stitched up from pieces of other chromosomes. These relationships are called syntenysynteny, which reinforcereaffirm the thesis that all living things came from a single linepoint of origin, if you go back far enough. Really, the fusion point of Chr2 is interesting because its a relatively new event; by picking through the pieces we might find some understanding of something that appears to be a common phenomenon in genome dynamics.