The way this would likely work in the offices of the environment commissioner—and I'm speaking from my present vantage point, not my previous vantage point—is that these would likely be performance audits, so value-for-money audits, non-financial audits. Within that area of the commissioner's work, there are, as you say, recommendations issued.
The way to perhaps modify Bill C-12 to ensure you get the meaningful recommendations you're looking for—assuming everybody wants this to be as strong on the transparency and accountability front as possible—would mean including language closer to that in Bill C-215, proposed on February 24 by the Bloc Québécois, which tied it to actually achieving the emission reduction targets. The present language in clause 24 is relatively loose, and so there is some text to revisit and pluck, perhaps, from Bill C-215.