If you watched the all 22 films you'd also see WRs getting open and the QB not throwing them the ball, like how Amari was killing Peters but Dak rarely went to him.
The two notions are not mutually exclusive. He still ran the staple route combinations and concepts just like Coryell drew up in the 1970s. It's been outlined ad nauseum since he has been here.
An athletic receiver that has a refined route tree is going to get open regardless of the system. If a DB cannot anticipate the route because of how it is run then the DB without help is going to get toasted.
The point here is that Cooper getting open speaks to Lal's aptitude as well as Cooper's own. It speaks little to nothing of Linehan.
What Linehan did not do is adequately use player's natural ability to scheme other guys open. All the attention the Beasleys, Dezs, and Coopers drew should have allowed Linehan to exploit so that others were schemed open.
Outside of lining up Jarwin on the same side of the field as Cooper and throwing him jump balls up the seam and on flags, you never saw that.
Really what strikes me about the limitations of Linehan's gameplans is his inability in 3 years to incorporate Zeke, who was coming out one of the best receiving NCAA RB to come out in the past decade, into the passing game. He tried various things like flexing him out and the odd wheel route but it met with underwhelming production.
At the end of the day, Cooper and similarly talented/skilled receivers are going to still get open. It's the rest of the offense wehre the issue comes in.