Debian solved this particular problem a long time ago, with pbuilder(1): packages that are installed "from source" simply get compiled in a chroot. Strangely, nobody has ever copied the idea.
The modern hipster-language equivalent would probably be to make the package manager depend on the presence of Docker/rkt/systemd, and use it to pull down a dev-env container and build the native bindings in that.
Nix/NixOS - everything is build not only in a chroot, but also in various namespaces. Of course that doesn't help if you actually use a package (directly or indirectly) hence executing it outside of the build chroot.
