If you want to have a house built in Japan, you have three basic choices: a large-scale "house maker" 大手ハウスメーカー, a local builder ("komuten" 工務店), or an architect ("kenchiku sekkei jimusho" 建築設計事務所). It's unlikely that any of these people will tell you about the other options since they have their own commercial interests in the way they do things.
An architect should be able to build anything you ask for, or at least will be able to draw it. There is a risk that you may not get what you want, either through miscommunication, practical issues or the fact that architects have their own agendas and aesthetics, and your house is one small piece of that jigsaw puzzle. Perhaps worse, you may get exactly what you want, but find when you move in that you didn't want that after all! Building through an architect will often cost less than a house maker, but there is no guarantee. This route will work best if you find an architect who shares your idea of an ideal home. If you can find an architect interested in building a low-energy house, with some experience in highly-insulated highly-airtight buildings, then it should come out cheaper and higher quality than the house makers. If you treat the architect as if you were commissioning a famous artist to create an artwork, then this will go smoothly. Smother still if you imagine the artwork will be displayed in a gallery that you can visit if you want to. Of course, back in the real world it's going to be a house that you'll be looking at it every day, and usually concerned about its function rather than its form.
Going straight to a komuten will give you more freedom than a house maker, but not as much as an architect, and they will probably be cheaper than either. A komuten will often employ at least one qualified architect who has all the technical skills and legal qualifications to build a house. Ninety percent of the building companies in Japan produce fewer than ten houses a year, so there is a very long tail in the construction industry. Finding the right one for you, in the right place, may be more tricky.
There is a grey area between architects and komuten, in terms of finances and project management. Architects do not build houses, and the construction of your house will probably be carried out by a komuten whether you choose an architect or a komuten. In fact even some of the large-scale builders contract work out to komuten, so it's possible that exactly the same people will be building your house whichever route you chose.
The basic role of architects is to design the building, and in the simplest case they will do that only, and hand over the plans to a builder. More often the architect will see the whole project through, and may act as the project manager. When it comes to payment, the architect may charge you for the whole lot, and subcontract the komuten and other contractors. Or you may pay the komuten and the architect works for them. In either of these cases there is one person to negotiate prices with, and as a customer it is clear who is responsible if something goes wrong. Which it probably will since houses are complex, and building is more art than science. Alternatively, the architect may charge a fee and you pay the komuten separately, but the architect will stay on to oversee the project. This may be less ideal.The carpenter is really important if you're building a wooden house, and in fact carpenters used to build houses in Japan without architects, and they are part of a long tradition. This may not always be a good thing if you want to build a low energy house since you sometimes need to go against building tradition. Many of the older people in the building trade have basically decided on the way things should be done, and it may be very difficult for them to try new approaches. In fact they may see new ideas as direct threats to their livelihood and will be hostile towards them. Younger people may be much more open to new ideas, but of course they have less experience!
Another potential danger is choosing a friend to build your house. You may feel a great sense of security relying on someone you know well since building a house is a daunting process. However, there is always a danger working with friends, and with as big an investment as a house, the danger is potentially very big. If things go wrong, then you may lose your friend. Even if things go well, you may feel that you are helping them as a customer by giving them work, and they may feel they are helping you by working for you, which could strain the relationship. If it is a very good friend, then your friendship may be too much to risk for something as trivial as a house, and if they are not a very good friend, you have no reason to choose them above anybody else. You should be choosing the people who are going to build the best house for you. Of course things may go smoothly, and it may turn out that your friend is the best person to build your house, but that should be the end point, not the starting point.
Note: In Japanese, Ichijo somewhat confusingly calls itself Ichijo Komuten, but they would not be described as a komuten. In fact they have operations in the US and Australia as well as in Japan.
