I'm noticing that mojarra outputs named html entities in many cases as opposed to numbered entities. This seems to cause issues when using an application/xhtml+xml content type. I looked through some mojarra configuration options but wasn't able to find a way to configure the application to always use numbered entities. Is this possible?
The standard renderkit of JSF is designed to output (X)HTML, not XML. You need to supply a 3rd party renderkit or to create a custom renderkit which outputs XML. No 3rd party ones comes to mind however.
Apart from that, if you intend to return XML upon a web request, then JSF is not really the right tool for the job. Better head to JAX-WS or JAX-RS.
By the way, the right XML content type is not application+xml but application/xml.