Sounds like as a general rule he's a good eater. But he doesn't like onions, tomatoes, and peppers. Which if you think of it, all have exactly the same texture when cooked. Which would be enough to turn me right off a plate, and I'm a non-picky adult!  Onion rings are deep-fried and crispy - completely different. But the texture of cooked onions, tomatoes and peppers is not an unusual thing to avoid.

All of our kids were allowed to pick  two foods that they didn't have to eat ever. No questions asked. No they did not turn out to be picky eaters, we just understood that just because everyone else in the family loves onions and cooked tomatoes doesn't mean they have to. It gave them autonomy I.e. control over their food.  Ironically, my kids picked out the foods you exactly described - cooked onions and cooked tomatoes and cooked peppers. Honestly, foods that if I served them at the table today in a family dinner of 16 people, three of them would still be putting those aside. I think this is a choose your battle moment. If in general, the child is eating vegetables and fruits and a general assortment of foods, not just chicken nuggets and french fries fries, pat yourself on the back you're doing just fine!

if you're worried about the example he's setting then you can make that rule for everyone. There are two or three foods that you don't have to eat. They get to pick them for themselves. Maybe one hates peas and the other loves them. Maybe one hates broccoli and the other loves cauliflower. But knowing for yourself which foods they as a rule don't want, maybe you can put their portion aside without adding it? Or allow them to pick it out without hassle. Chances are they will try them time and time again, and may eventually grow out of it, but not always. To this day, my sister not only does not eat onions, but it turns out she can't. She has a condition that makes onions unacceptable to her body, but I never would've known that as a child.

Eat what is prepared or starve.

KISS.

Time for a back in the day story.  There was a time where kids ate what was prepared.  Period. Dot.  
 

They didn't eat, their plate went in the fridge and that is what they could have until they ate it.  Even was better was the sitting at their place at the table until they ate it.  However long that may take.

We did not have to eat a bunch, but we had to eat a small portion of everything under the prime directive of "Take what you want but eat what you take".

An experience that highlighted this issue from my youth was an Embassy dinner.  My dad worked for the US Department of the Interior and was seconded to the State Department.  This dinner included families and was formal.  A kid at the dinner around  my age, about 9, didn't like the food and loudly list his shit about it as the parents tried to coddle him.  They did not immediately escort him or to deal with it and tried the ignore, coddle, comfort cycle to no avail.  After a few minutes an Embassy official approached their table and had them escorted out.  They all had to do the walk of shame in front of  the Ambassador, the VP of the USA and any number of host country officials.

That shit did not fly in my parents parenting model.

I hate onions, I always have. I hate any food that has any hint of spice or burn. I find that they physically hurt to eat. I didn't like onions or peppers as a kid. As an adult I still hate them, and I even have issues with tomatoes if they are too strong. I don't think kids should be forced to eat foods that they really don't like, or that even might hurt to eat. Adults don't eat food they don't like and I've always been puzzled as to why society thinks kids should eat food they don't like. I understand that kids can't eat nothing but sweets, but if there are a few specific food they don't like, I wouldn't make a big issue over it.

I say just let him eat around them. If he eats the meal but picks them out quietly then clears his plate and puts it in the sink/dishwasher, leave it alone. But don't allow the fake gagging and all that. As a picky eater myself, i know there are polite ways to eat what i like and leave the rest without being obnoxious about it. 

I think punitive tactics such as making a child sit there till he eats it, or keeping the meal in the fridge and presenting it again, are abusive.  When my daughters were children, I told them they could either eat the meal I cooked, or make themselves a sandwich. A 10 yr old can easily make himself a sandwich.  

Kids should be exposed to a wide variety of foods.. but they also should be allowed to have their own likes.. dislikes. preferences.. and no one should be forced to repeatedly eat things they actively dislike.  for him, it may be a texture.. and/or a flavor issue.  And.. that's fine... if he has given them a "good try".. a few times.. he gets to pick them out (if the meal can't be made with the items somewhat separately.  I might be inclined to make the pieces BIGGER in the dishes so that they are easier for him to exclude. possibly even for you to exclude them from his serving when he gets it.

I agree that the table manners as far as being able to quietly and without gagging deal with the unwanted items is what I would focus on.  I would also probably stop pushing him to eat these things.  If he truly doesn't like what you have served.. a PBJ sandwich he prepares himself is a fine alternative.  

Your younger kids can also have those options.

Again.. kids should be presented with a variety of foods.. and the requirement should be that they have to try them a couple times before they are dismissed out of hand.

You aren’t at a loss for what to do, stop putting those items in his meals, problem solved.  If your littles are even noticing SS isn’t eating certain things, then that is a great opportunity to talk about foods and how sometimes people can enjoy them one way and not another.  My BD was a super picky eater when she was younger, but it never affected her health, today she eats all types of foods and has found she really enjoys Asian cuisine.   If SS is healthy and not just eating junk food all the time he should be fine.