Let's say you're developing a python package that relies on a native shared library. If you distribute it as a pre-compiled wheel, you're locking your users into the exact version and compilation flags, options, etc that you choose. So your question effectively boils down to "why do people need to compile their own software?".
Many reasons: you need more control, specialized hardware, testing newer versions of the library, maintaining an internal fork of a library, security, performance, the dev team maintains both the native library and python package and needs to keep them independent, or simply preference for dynamic linking against system libraries to avoid duplication.
> So your question effectively boils down to "why do people need to compile their own software?".
No, the question is why a package would need to decide for its users that the package and its dependencies must be installed the gentoo way. That's quite obviously different from why an end user would decide to install from source despite the availability of binary packages.
Many reasons: you need more control, specialized hardware, testing newer versions of the library, maintaining an internal fork of a library, security, performance, the dev team maintains both the native library and python package and needs to keep them independent, or simply preference for dynamic linking against system libraries to avoid duplication.