Since apple trees CAN be started from clones (cutting/grafts) there is no reason to breed one to come true from seed.
The other issue is how pollen is transfered. Plants that rely on bees are very promisucuous in that pollen comes from far and wide, increasing opportunity for diverse genetic expression. In most tomatos (where stigma don't extend outside the enveloping flower petals) the pollen is released and remains within the individual flower, dramatically reducing the opportunity for cross polination, making tomato come unusually true to individual.
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