I`m no biologist, AF, but the fact that bacteria have intruded into other species to a limited (but life-necessary) extent, seems to point to multiple lines of abiogenesis. I imagine in a time of non-bacterial dependence, other species may have managed on their own, but I can`t conceive how they coped.
Im not sure what this means and I'm certainly not sure how it has any relevance to the question of whether all life has a common origin. No species need ever have been bacterially independent since bacteria would already have been there extant in the environment. By the time any multicellular life reached a size suitable for bacterial colonisation I should think it would already to be host to innumerable bacteria.
I'm assuming you are thinking of things like gut bacteria rather than things like mitochondria or chloroplasts, but its hard to tell from your post.
Morphology seems to point to different origins, too, with a large number of species having mouth, eyes and other sense organs in close proximity and excretory organs at a distance. Versus others that have evolved along different lines.
I don't see how modern difference present much of a problem for common ancestry. if the different morphologies were the product of different abiogenetic events then how do you explain the sharing of a common genetic material and code? Not to mention the sharing of many of the same genes. Why is it not more likely that they have evolved along different lines having diverged from a common ancestor?
TTFN,
WK