I'm going to give my opinion, but I am not a Buddhist or Taoist Master, therefore this is just a simple opinion (I am a student of Zen Buddhism with little experience).
Your question seems deeper than it looks at first glance. It is not just about bonsai actually. I will try to develop an example that could put some light into the question.
Let's say you are walking in the woods, and then you hear a cry from a little girl. You go to investigate it, and you see that the girl fell into a big hole in the ground, a hunter's trap. The girl cries for help. What do you do? You most certainly wouldn't tell her: "I can't help you, helping you is not natural, this is anti-uncarved block. Your destiny is to stay in this hole."
Ok, this example is very extreme, but it shows that still-action is actually action. Still-action has its consequences. What is the natural thing to do in each case? It looks obvious that helping the girl is the natural thing to do in my example.
What about the bonsai? To keep it healthy, you need to cut its roots, you need to cut the buds off ocasionally. If you don't do these, the bonsai will overgrow and may eventually die. The definition of bonsai is tree-in-the-tray, and for a tree to stay healthy in a tray/pot, it needs these especial technics to be applied. Applying them is the natural thing to do.
But you may say, why should a tree be dwarfed in a pot in the first place? To which I respond, why should a tree NOT be dwarfed in pot? Who says so? Why should all trees grow to their full size outdoors? Who says so? Is a small tree less special than a big tree? Is an indoor tree less special than an outdoor tree? Who decides what is natural and what is not natural?
Bonsai is useful. It is a patience exercice. Its gardening may be a contemplation exercice. It is beautiful. It is an artwork, and a live artwork, which responds naturally and freely to the artist's input. It's an artwork that instantly can be recognized to belong not only to the artist, but to nature as a whole.
Also, uncarved block is much more about mind than anything outside the mind. Therefore, a person can cultivate a bonsai with an uncarved block mind, but also with an un-natural mind, an articial mind, a mind that is arbitrary. The bonsai may not grow as you expected, and you become angry. That is un-natural.
Finally, you can go to a friend's house, see a bonsai there and think "that's un-natural". But this thinking, "un-natural", is only in your mind. Nature is already there.
I hope this can answer you at least a little bit.
