In a sense, that was the wisdom of Parliament. The legislation lays out that there are certain thresholds over which a project shall be assessed through a comprehensive study. The comprehensive study regulations define those thresholds; the agency simply implements them.
The decision on whether or not to move from a comprehensive study to a panel level, which of course is the most public process, rests with the Minister of the Environment. She makes that decision under law, based on recommendations from whichever federal departments need to issue the permit. It's really part of the legislative scheme.