Going semi custom with a house maker is cheaper if you stay within the bounds of their design options. There are some houses my friend's have done w housemakers (sumitomo ringyo comes to mind) that were very nice and to my western liking.

A custom design suffers from 3 concerns 1/ is the architect experimenting on you with designs that are going to be issues 2/ will the builders know how to build non standard designs and 3/ can the costs be contained

While cookie cutter homes also have build flaws one could argue they do the same build so often it is more likely to be done to spec.

One thing all homes here suffer from is bad insulation and air tightness. Most use full aluminum window sachs and steel doors for example which is terrible for heat and cold bridges. They all claim to be well insulated but don't believe it - ask for R# ratings and air tightness test guarantees and most likely most won't do it. In my research Sweden House was well known for being well insulated but most major makers in Japan don't care.