Dave, quite a diversity in the dimensions used for timber frame construction here. What you say about 100mm square might be a standard for certain parts of the more common houses, but i think that you also will find heavier elements commonly utilised as well. Budget is a real constricting factor, when the funds are there, the standards readily change. Slow growing Japanese cypress was a preferred material for a long time, beautiful stuff that really shines when planed, with Pine commonly used for larger members or sometimes hardwoods. Show off locations within, used the treasured Zelkova or something else special on occasion. The domestic high quality woods have become rather expensive, as you say, cheaper substitutes have become common. Temples and shrines, they still pull out the stops because of large budgets. The carpenters doing those aren't very common either, specialists and often two years or longer projects. One thing that is very noticeable compared to earlier, is that with the imported woods that are already dry, you don't see houses that only are framed and have the roof on, sitting to dry for a few months. Nobody around, you could check those places out. People nowadays actually think that's an advantage with the hurry up no desire to wait to move in any longer. When it comes to strength and resiliency, personally i'd much more prefer having air dried over kiln dried any day.
Your pegged joinery that you show is really very attractive and reflects high skill.