The linked bug is about an entire <template> with a <script> being inside another element's HTML so it's not related.
The behavior you observe here is correct and matches the specification AFAICT.
https://html.spec.whatwg.org/multipage/scripting.html#htmltemplateelement

A <template> element doesn't have any children so there's no point in setting its innerHTML.
You can use its "content" property:

    var t = document.createElement('template');
    t.content.appendChild(document.createElement('script')).textContent = 'alert("hello")';
    document.documentElement.appendChild(document.importNode(t.content, true));

In order to actually run a script you need to make sure it's not "inert" as defined in the above spec:
* create the script element manually via createElement 
* attach the script element to the live DOM

The specification says the only case when the scripts aren't inert is when the <template> was present in the original opened document so for example this test.html runs the template's script:

    <template id=tpl>
      <script>alert("hello");</script>
    </template>
    <script>
      document.documentElement.appendChild(document.importNode(tpl.content, true));
    </script>

Thanks for taking the time to explain this. Sorry for filing a bug about behavior which is correct!