Companion planting

As a newcomer to companion planting, I have been trawling through the many charts in preparation for my newly created edible patch which is made up of a raised bed, veg trig and several pots. Can I assume that this companion and enemy advice refers to planting in the 'same soil' or does it also apply to 'different pots in a close proximity?'  For example, apparently tomatoes detest dill, but if they were planted next to each other, in different containers, would this still be a no no?  I fully understand how plants with differing soil requirements and pest conflicts can be a problem but do some plants simply dislike being 'close' to others?  I really wanted to grow my recently germinated sunflowers, tomatoes and dwarf green beans but they are classed as antagonists to each other :(
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