One thing that isocaloric studies do not show is how chronic consumption of one particular diet or another influences consumption patterns over time. This is by design and is a huge flaw IMO.
Any diet that keeps you just above the limits of starvation is going to show no change in weight gain.
A much more compelling study would be an overfeeding experiment between a high fructose diet, high glucose diet, high protein diet, high fat diet, etc.
It seems like the author is really set on rejecting the conclusions of these meta-analyses.