It is how Webpack works, actually. Webpack does not support bundling to native ES6 modules [0], it has to bundle into a format which requires runtime code being injected to execute properly, handling imports, and whatnot instead of relying purely on native ES6 modules.
Have you ever looked at the contents of a bundle? [1]
Long story short, Webpack circumvents native ES6 modules in favor of other module formats. It provides a great amount of utility, but it is not Vanilla JS.
[0] https://github.com/webpack/webpack/issues/2933 [1] https://pastebin.com/C2qPunwV