I think it depends how far down the rabbit hole you want to go. Realistically, breeding apples for certain characteristics that humans desire is unnatural. Plants will always cross with other cultivars within the same species and hybridize, given the chance. In nature populations of tree in any given area would be likely to have quite similar genetics, since they have the same evolutionary pressures on them and have spread from the same genetics. But if one population of
trees grew close to another, different population of trees in nature, they would hybridize. So what is more unnatural is really the fact that there are all these different apple varieties we've bred, not hybridization itself.
Grafting is a separate issue - it is really just a way to propagate the same genetic material.
Dwarfing is another separate issue. You can graft an apple tree onto a non-dwarfing tree.
There may also be hardiness benefits to raising trees from seed in situ (even if you graft other varieties onto them), as they can then form a taproot, whereas transplanting damages this development.
Any apple you get anywhere has a chance of not growing true to seed, unless it has been grown only around other apples of the exact same genetics. It's a bit like your pumpkins in your veggie patch, you could end up with a dud if you let them cross pollinate. From what I have read you have a fairly good chance of getting an edible apple from your seed, but if not you can always graft another cultivar on. And the child seeds of your tree will be different again depending on what they get cross pollinated with.
In trees it is easy to cultivate wanted varieties through grafts, and this can be done by the home gardener in a nuclear winter if need be. Hybrid seed for veggies has quite a different production process where plants are grown in controlled conditions and the male organs of some of the plants are removed by hand so that they do not self pollinate, allowing the second variety to pollinate instead. This is often done in third world countries like Taiwan, where labour is cheap. Arguably it is not worthwhile without cheap labour, so in the future hybrid seeds may become far more expensive.