to stain or not to stain

These are the exterior materials, clockwise from top: red cedar for the hafu, the barge boards that are the finishing pieces at the end of the ridge ends; sugi cryptomeria for the shitami-ita, the wood siding; and the scraped off-white mortar.
Below are the same materials (clockwise from top: cryptomeria, cedar, mortar) after spending an evening testing a natural stain. The contractor wanted an answer soon, so I called him on Sunday morning to tell him that we're going to stain the wood, rather than leave it clear.