Ok I have reported back there in regards to stripping out shaders. But not sure if that will help me figure out the tree shaking problem I am experiencing.
It would be nice to use the elegant import system but it maps to the sources when making a three bundle. Instead its looking for multiple versions of npm three modules and bundling them in.
You can make it reference three for the import in a 3rd party module. And set the rollup config to three as global. That is fine it wont bundle three that way then.
But doing it the other way importing that module into a custom three bundle does not work.