Bottomline is it's advisory. Cooperating agency is a techincal term. It means they aren't the authorizing/approving agency. All they can do is advise, not deny. The tenor of the EPA letter is similar to much of what they've said over the course of the past four years. 

Of course, LAC should want to do much of this...and, I expect they are. 

Bottomline is that this doesn't change anything. It does, however, reinforce that approval is coming.