The main difference between shipping a binary and a js file, is that users don't expect binaries to be small, which means you can usually ship an entire runtime with your binary. If you shipped every single js polyfill with your website performance would tank. You also generally differentiate between downloading a binary and running it, and users will tolerate a loading spinner while a massive binary downloads.
Webpack will emit a warning if any of your build artifacts are larger than 244KB, whereas a 244KB binary would be considered anemic.
Binaries were definitely leaner in the past, but there's always been that dichotomy between downloading software and running it.
In the browser, users expect software to be available instantly, and that constrains how you build webapps. Users will tolerate the google maps app taking a few minutes to download, but they won't accept the google maps webapp taking several minutes to load in a browser.
