The complaint is that if you strip the controls out, then you're no longer betting on diet. Because whoever maintains a fully plant-based diet is drawn from a population that 'probably' smokes less, drinks less, sees doctors, sleeps, blah blah. True.
But nobody constructs elaborate arguments about hypothetical Oreo-vegans because they're worried about hypothetical Oreo-vegans. The same person who wants a randomized control trial about how 'healthy' a plant-based diet is versus an omnivore diet will happily take creatine on the strength of a forum post.
A thought experiment: bet money on who you think will live longer. Someone vegan or someone who isn't. No whining about controls like "how well planned is the diet", how much they exercise, if they smoke, and so on. Just a deadpool bet at a dive bar.
Ultimately, I've never found any of this research showing that vegan diets are good for you to be worth the controversy. It's not that 'veganism' is intrinsically better than eating meat. Fiber up, saturated fats down, and so on, and a vegan diet is a very good implementation of it. I have a feeling the reason why it makes peoples throats so tight has nothing to do with health.