I tried installing the project’s dependencies locally using yarn install --production, after purging node_modules. When running npx @netlify/zip-it-and-ship-it@beta server/dist/functions dist-zip, it creates a ~40MB bundle instead of a ~70MB one. The latter gets built when running yarn install regularly, as it resolves to @netlify/zip-it-and-ship-it@0.4.0-7 (beta) instead of @netlify/zip-it-and-ship-it@0.3.1 (latest). The beta seems to work fine, while the latest seems to produce wrong output.
I’m not sure about which one is used by Netlify’s cloud services, but in this case, the beta seems to outperform the latest package.