I very rarely pinch the tops out of my tomatoes i just feed them well and let them keep going however to get better trusses it is better to pinch them out after 5 or 6 trusses doesnt really matter how tall the plant is.
Onions should be fine in a container give them 4-6 inches between the sets depending how big you want your onions and i see no reason why you cant sprinkle some carrot seed between them as long as you keep the container well fed
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