I figured that you would be considering this. Anyways, things like transplanting a sharingan/senju DNA would be considered unnatural depending on the circumstances. If its without the person's consent, and only used as a way to gain more power then it is a form of artificial enhancments.
There are certain circumstances, however, when that it is considered ok due to it being necessary in order for a person to continue their natural growth.
Such instances would be like kakashi receiving the sharingan from Obito. Without an eye, he would be at a serious disadvantage against other ninja, so therefore, because Obito offered for him to use his eye to help him, he was able to continue to become stronger naturally with the added benefit that the sharingan grants him. Now, with this added benefit there is also a side effect to this. Because Kakashi is not an uchiha, the sharingan drains him much more quickly than usual, making it a jutsu that he can only use as a last resort.
As you can see, in order for a specific alteration to qualify as natural, it must be: done through the user's consent, done as a way to cover for a severe handicap that one would normally have without it when confronting any normal shinobi such as an injury/illness, and it must also have an equally heavy drawback that keeps the user from taking advantage of its benefits too often.