MorganaXProc is pretty close to XProc: An XML Pipeline Language. W3C Recommendation 11 May 2010. This page is to mark deviance from the Recommendation. The entries are ordered by step names, so you can easily find the information you need.
The option "dtd-attribute-values" is not supported. Using the step with option value "true" will result in a XD0030 error.
If you are using the standard XSLTConnector (TraxXSLTConnector), options "initial-template" and "initial-mode" are not supported because the classes in "javax.xml.transform" do not support the setting of an initial template or an initial mode. However if you use one of the other XSLTConnectors supplied, both options will work as expected.
MorganaXProc does not support XML 1.1.