Finally fixed it, I think it was coming from a misconfiguration of Webstorm. I followed the doc on Jetbrain's website. In particular I took the time to properly configure Language Services for TypeScript and run configuration, I use ts-node on the produced JS code.
There seems to be no need to use npx tsc --init, to generate the package.json and tsconfig.json one can simply create the files from the Project window.