Hi Polymerase,
Starting with the next Chrome Canary, Custom Elements in templates aren't going to be "live." This means Custom Elements in templates are more like <script> and friends--inert.
This means if you're pulling content out of a template and you want the Custom Elements in the template to pick up the definitions registered with the main document, instead of
var goodies = myTemplate.content.cloneNode(true);
// do something with goodies
you should do
var goodies = document.importNode(myTemplate.content);
// do something with goodies
Technically, the template document has its own set of definitions, so you could set up Custom Element definitions there with myTemplate.content.ownerDocument.register(...). But you probably don't want to do that.
I'm happy to take questions, feedback.
Dominic