I think the important thing in considering an answer to your question is that the government was very conscious of the need not to create additional bureaucracy, which is why they chose to strengthen an existing entity of Parliament--the Library of Parliament--and use the existing resources and capacity and expertise there and simply augment that to provide a new service for members of Parliament.
The function of the parliamentary budget officer is designed, essentially, to be one of research to support members of Parliament, which is a very different role from that of the Auditor General. I think the government's decision to locate the parliamentary budget officer function in the Library of Parliament reflects a better matching of mandate than would be the case in the Office of the Auditor General.