As you pointed out, it's currently a program administered by Industry Canada. As a public servant, I would say that it is less expensive to administer FedNor because the administrative overhead is shared by the entire department.
If you consider each of the other agencies, you will note that they all have a human resources section. They all have a financial affairs section to handle overhead.
Within Industry Canada, this overhead is shared by the department as a whole. The lines that Parliament votes for for FedNor go more toward operations than overhead.
Also, the other agencies have a deputy minister and a bureaucratic machinery supporting them. I think, when you come right down to it, the agency functions with the independence it needs to achieve its own objectives.