For those cases where it's a custom element you're registering simply check that an element by this name hasn't already been registered. Obviously you can include more complex logic to vary the name, decorate the class, etc, however this simply checks to see if something is already registered using the existing API and if not, registers the given thing (in my style--yours can vary, this is simply showing how to generally avoid the error):
customElements.get('the-element') || customElements.define('the-element', HTMLTheElement);
For more on the API see https://developer.mozilla.org/en-US/docs/Web/API/CustomElementRegistry
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