The benefits to native bundling are
huge. I really cannot overstate how much they will improve UX, and DX.
The core web file formats: JavaScript, CSS, HTML, and images, do not have native multi-file bundling support. Today's bundlers have to jump through serious hoops, which drastically reduces the effectiveness of the network cache, to emulate bundling. And those hoops bring constraints that limit the native features of the web platform that are usable with bundlers.
JavaScript is bundled by significantly rewriting it. At the very least imports and references to imports have to be rewritten. Live bindings from modules require special care. Dynamic import() is severely restricted. import.meta.url usually doesn't work well, or at all. Base URLs for all resources are changed, so getting assets with new URL() and fetch() is usually broken. That causes bundlers to support importing module types that the browser doesn't support, so at development time you still have to run the bundler. The whole thing just diverges from standard semantics.
CSS is bundled by assuming a global CSS scope so that the individual files are not needed separately. URLs within the CSS have to be rewritten. The upcoming CSS Modules specification allows JS modules to import CSS, but since you need to import the actual stylesheet you want, and CSS doesn't have it's own multi-module support, you really need native bundling to make this work well in production.
Images can be bundled _sometimes_. Maybe a spritesheet will work, or data: URLs. It all depends on how you're using them.
It's all a complicated mess that requires complicated tools and WebBundles just fix it all. You no longer have to rewrite any references in any files. If you do build files, it's purely for optimization, not because you have to.
What's important for users is that files in a WebBundle are individually cached. This makes it finally possible to do delta-updates on pages where you only send the updated files. Maybe the initial visit is with a bundle and subsequent visits use HTTP/2 push. Maybe when you deploy you build delta bundles against the previous X versions of the site. With current bundlers only the bundle is cached so you can't do this at all.