I accept the fact that organelles like mitochondria, chloroplasts, and possibly peroxisomes are descended from originally independent organisms, but none of these seem to me to be essential, defining features of a eukaryotic cell.
Indeed, the classic defining feature of a eukaryotic cell is that it has a membrane bound nucleus. It has been suggested that the nucleus itself could have an endosymbiotic origin. The order in which different characteristics of modern eukaryotic cells originated is pretty controversial. Lynn Margulis, one of the major proponents of the Serial Endosymbiotic Theory, puts forward a hypothesis where the initial symbiotic event was fusion with a spirochaete giving rise to a proto-flagellum and that as a consequence of this initial fusion the nucleus arose from the dissociation of the incorporated organisms enveloped genetic material from the proto-flagellum (
Margulis et al., 2000).
I'm not sure that what Dawkins means is anything more than the 'community' of incorporated prokaryotes involved in endosymbiosis when he discusses colonies, i.e. a modern eukaryotic cell is a 'colony' of, albeit simplified, bacteria in the same way that he describes an elephant as a colony of eukaryotic cells.
I think that what Dawkins is describing is exactly the same as endosymbiosic theory, so I'm not sure why it wouldn't explain exactly the same things.
I don't see anything to get upset over.
TTFN,
WK