I'm not certain you're interpreting the content of both games correctly.
In EU, the Uber Ethereal admits to the Volunteer that they're the ones who "failed to ascend", implying that they are the members of the biological Ethereal species that failed to reach the, well, ethereal form we've seen in the Bureau.
Upon failing, the ones left behind started to search for a substitute, a strong physical form that could also contain the Gift. It's likely that the same personal shortcomings that kept the remaining Ethereals from ascending were also responsible for their different approach to "advancing" other species. Instead of the subtle manipulation of the Bureau Ethereals, the "failures" callously terrorize, control and engineer other species with a complete disregard for their own intelligence.