I'm pretty passionate about physical fitness and body composition and would recommend the following sources/figures to follow:

Menno Henselmans (known for "bayesian bodybuilding", website)

Mike Israetel (co-founded RP (disclosure: I intern here), wrote these books of some potential interest). I'm a friend of Mike's and can also vouch that his thinking style is very rationalist-adjacent.

Eric Helms (founded 3DMJ and wrote these books which are great)

Lyle McDonald (good FB group here, website here). Lyle is extremely abrasive, but he knows his shit. He's also not afraid to call out other figures in the industry for what he believes to be inaccurate info- I'm personally not a fan of his discourse style but again, he knows this stuff back to front.

Greg Nuckols (website, great intro books here). Greg is fucking awesome, super rationalist-adjacent in thinking style and discourse.

If you want my number one recommendation for books/resources, it would be to get the Art and Science of Lifting books that Greg co-wrote (linked above). The Muscle and Strength Pyramids (linked under Eric's name) would be a little bit more thorough treatment of similar topics. I'm personally a fan of Mike/RP's training and dieting methodology, but all of these guys agree on the most important elements of training and dieting and nuances beyond that are pretty irrelevant in the grand scheme of things.

Stephan Guyenet - uses evidence and careful reasoning, well versed in Bayesian updating as can be seen with how his views have changed overtime. I have a lot of intellectual trust for Stephan. Body comp / sports are not his area of focus, but the foundations are the same regardless of the specific goal.

If you're willing to put a good deal of effort into this, I suggest Staffan Lindeberg's book. There's a good deal that can be inferred from his evidence from very different cultures with different disease rates.

Beyond that, I like Chris Masterjohn, Dale Bredesen, Stephan Guyenet, and Chris Kresser.

This answer is for a skinny guy who wants to gain muscle. It may not apply to jacobjacob, who mentions losing fat too.

I prefer Lyle McDonald's exhaustively pedantic blog for a comprehensive theoretical foundation on general athletic training. A comprehensive theoretical foundation and a practical instruction set are different things. After going on and on about details, Lyle McDonald recommends Mark Rippetoe's Starting Strength course for practical strength/muscle building. I, a (formerly) skinny male in my 20s, found Mark Rippetoe's simple Starting Strength course to be extremely effective when I combined it with GOMAD. GOMAD stands for Gallon Of (Whole) Milk A Day. You eat normally (or more than normal) plus you drink a gallon of whole milk each day. GOMAD is cheap, simple and satisfies the most ridiculous protein and calorie macro requirements.

1. All that really matters is you get enough protein and calories. Are you a lactose-tolerant skinny male in your 20s living in the USA who has trouble putting on weight? If so, then GOMAD will get the job done. It is cheap, simple and effective. (A little creatine supplement wouldn't hurt but isn't critical.) If you are not a lactose-tolerant skinny male in your 20s living in the USA then IDK.
2. If you are skinny guy who wants to gain muscle then barbell lifting is usually the best way to do this. There are several slightly different routines you could achieve similar results with. Mark Rippetoe's Starting Strength is one course you could use. But you don't have to use his. Anything is fine as long as it features high intensity low reps of deadlift, back squats (or similar leg exercises) and pressing motions (overhead press, bench press, etc.). A pulling motion like chin-ups is good too but not quite as important as the others.

There is a Dr. Greger whose speech I can't stand but from whose books and online videos I have learned a lot (search for nutritionfacts and How Not To Die. Also, there are many, free online courses on health topics like the microbiome, epigenetics, diseases, nutrition, etc. that you can take through the years as they keep getting updated with the latest learnings (currently in vogue is the role of the microbiota in the gut, for example, so every few months new information is made available). What I've learned is that the human body is incredibly resilient and you can live several decades without major problems on the worst of diets, it's the accumulation of stuff over time that leads to what are now called Lifestyle Diseases and the ones it sounds you are concerned about: cancer, Alzheimer's, diabetes, etc.

Since we now know the body is an ecosystem consisting of smaller ecosystems and embedded in larger ecosystems, the interactions are too varied for anyone to predict what the best thing for you to do is. Statistics and studies only apply to large groups and always have outliers anyway. Some basic trends are useful, however, so you can look at which general lifestyles tend to produce fewer problems: moderate exercise, low intake of animal protein, lots of fresh vegetables, legumes, and nuts lead to healthier lives. Your best bet is to support what evolution has already solved for you and understand human activities and lifestyles through history (not the last several thousand years, mind you) and see how you can reproduce the conditions to which human bodies adapted to within the confines of modernity. Really, exercise seems to be the single most potent and underutilized method of becoming and remaining healthy, so kudos on asking for advise.

I one last ramble: supplements are only necessary when you have identified a specific deficiency and you can't address it through your daily nutrition. Vitamin D3 comes to mind if you live away from the equator and don't eat fish skin.

This may be a result of my personal bias, but my view is that the whole world of diet studies and advice often does not produce the results its consumers desire because of complex individual genetic differences that influence metabolism. And there may be additional influences from gut bacteria and epigenetics that also influence this process.

I think the long term answer to this question of "what do I eat to achieve the body composition I want" will be to get a 23 and me test and run it through some software that gives you a customized diet based on your genetic profile.

That being said, if I had to recommend any expert, I guess it would be Dr Aaron Carroll, who runs a YouTube channel named Healthcare Triage that essentially reviews research on various health-related topics.

There is a Dr. Greger whose speech I can't stand but from whose books and online videos I have learned a lot (search for nutritionfacts and How Not To Die. Also, there are many, free online courses on health topics like the microbiome, epigenetics, diseases, nutrition, etc. that you can take through the years as they keep getting updated with the latest learnings (currently in vogue is the role of the microbiota in the gut, for example, so every few months new information is made available). What I've learned is that the human body is incredibly resilient and you can live several decades without major problems on the worst of diets, it's the accumulation of stuff over time that leads to what are now called Lifestyle Diseases and the ones it sounds you are concerned about: cancer, Alzheimer's, diabetes, etc.

Since we now know the body is an ecosystem consisting of smaller ecosystems and embedded in larger ecosystems, the interactions are too varied for anyone to predict what the best thing for you to do is. Statistics and studies only apply to large groups and always have outliers anyway. Some basic trends are useful, however, so you can look at which general lifestyles tend to produce fewer problems: moderate exercise, low intake of animal protein, lots of fresh vegetables, legumes, and nuts lead to healthier lives. Your best bet is to support what evolution has already solved for you and understand human activities and lifestyles through history (not the last several thousand years, mind you) and see how you can reproduce the conditions to which human bodies adapted to within the confines of modernity. Really, exercise seems to be the single most potent and underutilized method of becoming and remaining healthy, so kudos on asking for advise.

I one last ramble: supplements are only necessary when you have identified a specific deficiency and you can't address it through your daily nutrition. Vitamin D3 comes to mind if you live away from the equator and don't eat fish skin.