I'm only an aspiring biologist, myself.
Endosymbiosis doesn't necessarily imply phagocytosis - it could develop from parasitism, for example. As I understand Margulis's original idea it was suggested that the original cilia cells would have lived as external symbionts in a colonial arrangement and then, over time, become more closely joined until they formed the arrangement we see today.
I don't think Dawkins meant the term 'colony' to be taken in any technical manner but simple as a group living together.