Hmm, seems like a logical extension of her serial endosymbiosis theory. However, whereas there's a lot of good evidence for SET at the microbial level, it sounds like she may be extending that beyond what can be supported. Not saying I disagree - I admitted I haven't read "Acquiring Genomes" (the only two books I've read of hers are "Symbiotic Planet" which was mostly new-agey philosophy with a dash of science, and "Microcosmos" which was fascinating and dealt with SET mostly). Obviously, to be able to argue the case one way or the other I'm going to have to read the book. (*grumbles*, another bloody tome on my reading list - maybe I'll pick it up before my next trip).
I would caution you about Margulis, however. Her ideas are extremely interesting, but she occasionally gets very assertive and positive sounding in areas which are not really well-supported. IOW, she's been known to overstate the case - a lot.