Without a prepare script, installing three as a git dependency (instead of from npmjs.com) will result in the certain files not being built, therefore installing from a certain commit will result in some code being up to date (in the src/ folder) and some code being out of date (f.e. build/three.module.js).
The script should be
"prepare": "npm run build && npm run build-examples",
if I understand correctly. I’m not sure what else is needed; there is not a publish script in package.json that would normally inform this.
@makc3d I’m blocked from the GitHub repo. If you can make me collaborator on your personal fork or a new fork just for this (or I can PR against yours), then I can provide patches there, and you can forward to three.js repo.