You might be able to fix that with something like babel-plugin-lodash which can be ran over your code (and deps) to enforce cherry-picking across the board.
To my mind, the "semver way" would be to make tree-shaking an option on a new minor version. After some number of releases, it might become a default on a new major version, if the maintainers so chose. Splitting the project into multiple codebases is not required by semver.
