When an element which imports paper-styles.html is loaded with importHref then custom theme settings get destroyed.
For example:
I have a basic custom theme defining just the value for one variable
<style is="custom-style">
:root {
--default-primary-color: #ff0000;
}
</style>
In static.html this variable changes the color of a paper-checkbox as expected to red:

In failing.html I use importHref to import the paper-checkbox
Polymer.Base.importHref('../paper-checkbox/paper-checkbox.html', function (e) {
var cb = document.createElement('paper-checkbox');
cb.checked = true;
document.body.appendChild(cb);
});
and now my-theme is overridden by paper-styles and reverts the checkbox color back to indigo

I understand why this currently happens.
I think paper-styles should not be able to just revert my custom theme settings.