First of all, there are shakuhachi instruments and then there are bamboo flutes that are shakuhachi-like. My discussion here is about well made shakuhachi instruments.
In general, root end shakuhachi usually have a tapered bore profile that narrows towards the bottom. This helps the second register play in tune and adds to the dynamic shakuhachi sound. However, not all root end shakuhachi display this tapered bore profile nor may they be tapered in the desired way so the luck of nature plays a small yet significant role in Jinashi making. Shakuhachi made from the upper part of a bamboo may play well if it has bore work done to it. This is something I call Spot Tuning. In General, every shakuhachi needs some Spot Tuning. Only the maker knows how much.