You cannot eat the leaves of a tomato plant they are poisonous but you can eat the fruit all day long. You can eat the stalks of a Rhubarb (mmmm) plant but the leaves are poisonous.
You can eat the leaves of tomato, its a myth that they are poisonous- they just taste like goat vomit boiled in a rusty iron pot
The primary alkaloid responsible for that, tomatine, is also in green tomatoes and theyre edible too, just... goat vomit. Frying, fermenting, or ripening the fruit breaks down the tomatine enough to remove the metallic bitter taste.
You got the music partly right tho, in some plants toxins are confined to one location. But in others they are transported, and in some a precursor is made in one spot and transformed further in another. Take tomato and belladona. A tomato grafted to belladonna stock will make deadly tomatoes, but grafting belladonna to tomato will reportedly make nearly non-toxic belladonna.
The point is its unknown how a situation in which Psychotria were grafted to kratom would play out. It would seem unwise, or at least hazardous, to make the gamble.