That's great, but it ain't there yet. [0] Incidentally, releasing a version 2 without deprecating version 1 seems a bit of a project smell... It might be the right thing to do in a particular situation, but what happened on the project that led to that situation?
Whole versions don't get deprecated. Visible features get deprecated when they are still present in the latest version but will be missing or incompatible in the next major version.
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.
[0] Tree shaking completely broken? #2867 https://github.com/webpack/webpack/issues/2867