I'm not in disagreement with you, but there is another aspect to consider.
In the case of many of these structures, their physical form is a reflection of some spiritual aspect. They're basically religious icons. Their design may be carried forward in part just because not doing so would be disrespectful on a spiritual level, or because they remind people of something. But they're not all the same.
There are probably thousands of different torii gates with slightly different designs. Some show an extended nuki with kusabi wedges, a modified mortise and tenon style joinery. But many torii gates don't feature these. Nuki joints are actually widely used as ornamental carpentry, and can be found in several non-wooden objects.
The construction of most torii, regardless of their material, seems to be about aesthetics (and honoring whoever paid to put it up) before the rest.
If you want maximum accomplishment with a material, check out their multi story pagodas that use a massive wooden beam in the middle. It acts as a mass damper and prevents the different floors from sliding off the building during an earthquake, as they aren't attached to each other. Hard to do that with stone! :)