It does get easier to address at scale. When applied to construction, the at-scale approach used to increase predictability is primarily available through a) pre-fab construction under conditions approaching control b) repeat buildings, the classic cookie-cutter houses. There's a reason why they're popular with developers.
A custom house will take longer and cost more than the estimate, on average. There is research on this in both small-scale and large-scale construction.
As a personal anecdote, I & partner built our own permanent dwelling (check my posts). It went over time and over budget, and even then, we had to compromise on features.
Don't forget that central heating /AC and "proper" insulation are not a standard feature in Japanese construction. Neither are cellars nor sound-proofing. Their plumbing is rarely winterized, and they often have the classic approach of kitchen on one side of wall, bathroom on the other. That's one bathroom, and a much simpler plumbing setup than multi-units popular in Europe or the US. These are just some factors in a long list that significantly simplify projects in Japan and make pre-fab a strong contender.
The Japanese consumer expects less and pays the same if not more.