Following discussion with @griff-rees: currently a package.json is created in the web app path upon running the template. Similarly a pyproject.toml and Cargo.toml are generated for Python and Rust backends respectively.
It may additionally or instead be advantageous to create a top-level package.json in the repo root to capture the script functionality. Adding further documentation to the README.md upon creating the template is also an option. E.g.:
cd web
pnpm i
pnpm rust
pnpm build