Well, I can’t answer why there was no support for the compiler from the very beginning, because I do not work on Polymer itself, but I know that there are people who are working to get Polymer to work better with the compiler. In the short term, we want to add such external effects:
https://github.com/Polymer/paper-checkbox/tree/master/externs
for existing elements and is studying the addition of externs generator, so we do not need to manage them manually. In the long run, we hope to get full support for compiling Polymer elements and ensuring that they work well with other compiled code. Will external intruders use your use case in the short term? Perhaps we can try to prioritize certain elements, or at least give you some idea of when they will be done.