@jcfranco My first question would be why would you need to style the placeholder node of the custom element? Once the CE is hydrated and rendered, then it is appended to the placeholder node so styling the root of the widget should be all that is needed.
As a proposal for v5, I think an additional option per element for @dojo/cli-build-widget to define an element as inline or inline-block makes sense. In the custom element handler we can then add the appropriate style for you. This could then still be overridden by a user with !important if needed.
In the mean time using the element selector like you put in your original issue seems reasonable 👍