Don't know if this title describes the wish correctly, but here goes:
Currently the configuration for the Storybook UI (React version for example) can cause conflicts with the rendered stories.
The biggest issue I have with this is when building preact components you can't mix them with react components (using preact-compat) because the react version used in Storybook is incompatible with preact-compat.
But I can imagine the same issues can occur with babel and webpack versions.