Skate will replace it after its rendering cycle.
Building cross-framework components with performance in mind, a web component thesis

This is a side effect of the functional rendering pipeline inherited by Incremental DOM. There are notes about this early on on the docs, but we should probably do a better job about highlighting the render() issue. Disabling shadow DOM will probably never be a recommendation, though, as this hides the implementation details of each component making top down rendering seamless and not prone to these errors.