My honest read of the study is that it's a poor attempt at making a case that sets out to prove something, ignores several variables that disprove its central hypothesis (like weight loss) and then steam rolls the idea that its showing something it absolutely is not.
The study, like all similar IF studies, showed that people who do IF sometimes are able to use it to consume fewer calories. That is important from a compliance standpoint: it means you can use this diet to treat obesity for some portion of the population for whom it is going to be effective because it will get them to comply with not eating too much. Not eating as much is associated with weight loss which is associated with all kinds of good outcomes. That's awesome, but it doesn't mean that metabolically there is something significantly different going on outside of eating less.
This is an important discussion in nutrition in general, and shows up in IF as well as keto discussion frequently, with proponents of each arguing that beyond the compliance aspect, there is also something special going on with your metabolism (ie: insulin sensitivity and other metabolic markers). The problem is that all of these are things that improve when you are in a caloric defecit, and the studies never disambiguate between the effects of a caloric deficit and the meal timing itself.
Fung makes the same mistake the authors of the paper do in interpreting their own results too optimistically. The dietary controls are set up in a way to make it seem convincing in an abstract if you are familiar with this area and what the current core issues are, but it is not at all if you dig in.