The SAXParserFactory.newInstance() method is used to create a new instance of a SAXParser. There are a handful of steps taken to find a SAXParser to use, as documented in the newInstance() JavaDocs. The problem with this is that Daffodil sets the entity-resolver property to an instance of the DFDLCatalogResolver, which extends a specific Xerces XMLEntityResolver. In order for this to work, we must be guaranteed that the SAXParserFactory instance we get is the Xerces one, and not some other one overridden by one of the ways described in newInstace().
So instead, we should use the newInstance method that lets you provide a string specifying which factory class to use, and specify our Xerces one.