I linked 4.1.0-beta.12 to package.json. The downloaded node_modules/babylonjs folder does not seem to contain babylon.d.ts refered by its package.json but instead babylon.module.d.ts. For that reason the typescript definitions are not available.
Editing the manually the package.json typings line to the following worked:
“typings”: “dist/preview release/babylon.module.d.ts”,