There is a confusion how Fukuoka san was planting his mandarin oranges and whether he was pruning it. So just digged Natural Farming book and here are the references I found about this.
"Everything is resolved then if we let the tree adopt its natural form through natural farming. The only problem that remains is how to induce the tree to grow in its natural form. Simply abandoning it leads only to failure. Before being abandoned, my citrus trees had been trained and pruned into a wineglass shape. The trees had an unnatural form from the moment they were transplanted as saplings. This is why, when left unpruned, they did not return to a natural form but became instead increasingly deformed."
"Obviously, the proper way to grow a citrus tree having a natural form would be to plant the seed directly in the orchard. But the seed itself, if I may press the point,is longer truely natural. This is the product of extensive cross-breeding between different varieties of artificially cultivated citrus trees, if allowed to grow to maturity, the tree either riverts to an ancestral form or produces inferior hybrid fruit."
"Direct planting of the seed, therefore, is not a practical option, for fruit production.Yet this is very helpful in gaining an idea of the natural form of the citrus tree."
"Creating a pure natural form is not easy, and the tree may deviate from this if adequate attention is not given to protective management at the seedling stage. This can be corrected in part by giving the tree a modified central leader form. To achieve an ideal natural form,the tree must be grown directly from seed or a rootstock tree grown in planting bed and field grafted."
In summary, it looks like Fukuoka san clearly understands growing orange from seed is not a viable option, so he also suggest to graft it, but grafting is done in the field. Also he observes closely the natural form of the tree and prunes it to take that shape so that further pruning can be avoided or minimised.