Fukuoka says quite a bit about how he prunes in Natural Way of Farming. I have the pdf version so I'm referencing those pages.
See:
3. Fruit Trees (pg 159)
The Argument Against Pruning (pg 172)
The primary discussion is that pruning
should only be done to encourage the natural form of the tree, the form in which branches do not cross haphazardly but are evenly spaced, and there is a main leader growing straight up. He goes into detail that exactly what the "natural form" is has been forgotten over time due to scientific pruning strategies, so we do not even know exactly what a natural fruit tree should look like. In general, a central leader (vigorous, upright leader) with an overall conical or triangular shape is the correct natural form. The tree should only be "trained" to the natural form for the first 5-6 years, after which the need diminishes. The tree is trained to the natural form by nipping off unnatural buds.
A tree will naturally create a form where each leaf receives sunlight, branches do not cross, and air can circulate. A tree would not naturally tangle itself up and create conditions for disease, or trees would not have survived for so long before humans came along. If the tree is pruned irresponsibly, the tree creates many buds at the cut point which then create an unnatural situation.
It is a similar argument as those against tilling, weeding, pesticides, and fertilizing. By performing these actions, man is only creating more work for himself later on, leading to endless toil. A tree improperly pruned, must always be pruned and tended to. Soil tilled, must continue to be tilled to break up compaction. Pesticides destroy the food web balance, inviting more vigorous pests. Ect...