I haven't gone through the paper in great detail, but at the very bottom, under "Competing Interests", you can see that the main author of the article "reports a grant from the North Dakota Beef Association to study the impact of diet quality on the relationship between red meat and human health", as well as other links to the agricultural industry.
The study looked only at one specific plant-based "meat" and compared it to the ground-up flesh of dead cows. I wonder why they didn't look at more plant products. Their conclusion seems to be that plant products are not exactly the same as the animal products they imitate; there are metabolites that are in the animal product but not in the plant product, and metabolites that are in the plant product but not in the animal product. Of course, since people who eat animals also eat plants, the metabolites that are missing from the plant product could pose a bigger problem for vegans than the metabolites that are missing from the animal product would for people who eat animals.
On p. 6, they say that "creatinine", "hydroxyproline", "anserine", "glucosamine", and "cysteamine" were in the animal product but not in the plant product. (Creatinine is, according to my Google search, "a waste product produced by muscles from the breakdown of a compound called creatine" and is removed by the kidneys. I think they meant to say "creatine". )
According to the following article (which seems to have a strongly pro-animal-flesh bias):
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088015/
plants do not contain the metabolites "taurine, carnosine, anserine, and creatine". When I look up these metabolites, I find many medical web sites that mention the good things they do in the body and list the animal body parts that contain them, but I can't find anything that states whether they are necessary. In other words, they may have been found to have benefits, but does a deficiency actually cause problems? (If so, I'm not sure how the researchers would explain the health of people who have been vegan for decades, such as David3 on this forum.)
Upon further thought, it is possible that our bodies, like the bodies of other animals, make these metabolites, and that we don't need to obtain them from the foods we eat. I tried looking up the four metabolites I mentioned above, and it looks like carnosine, at least, is metabolised by the bodies of cows but not humans. The question is whether it, and the other missing metabolites, are essential. I suspect they are not.
I am not a biologist (I was trained in a different science). You might want to contact nutritionfacts.org or pcrm.org to request that Drs. Greger and/or Barnard answer this question.