The solution for now is to rely on package management to resolve Polymer to a single compatible version for a project and its dependencies, and HTML Imports to de-duplicate loading of dependencies from multiple sources.
If you vend your elements as Bower packages, then a site can include them, with their dependencies and imports of Polymer, and if a compatible version of Polymer is available, use that one version across the whole project.
In the future version of Polymer, after ES6 modules and loaders are fully spec’ed, we will probably have a version of Polymer that’s only exported via modules so that multiple versions can be scoped to their explicit imports and can safely coexist on a page.