If you look at the eukaryotic cell it is certainly very different then a prokaryotic cell. As in Winstons paper a third hypothesis is common design. Common design based on the observed differences would favor separate origins.
When you look at the probability of a prokaryotic cell forming in nature it refutes the analysis. When you look at the probability of a prokaryotic cell evolving into a eukaryotic cell it also refutes the analysis as you have to account for the origin of very complex protein structures like the spliceosome. Common design seems to be the only rational inference.