Fix custom element pop-in with KeepElements disabled.

[dmccrthy]

Currently when the KeepElements flag is disabled the effected elements aren't removed from the HTML, but instead removed programmatically with JavaScript. This has an unintended side effect that even when KeepElements is disabled, custom elements still need to wait for the Javascript to load for the elements to render on the page. I'm going to put together a pull request for this but its kind of annoying.