There are many ways to set options [1] but it is not clear to me which one wins in the case where different values are specified for the same option by the different ways.

I guess it is the 1st one to be set. So SystemProperty, then command line, then .basex? 

I am often getting caught out by the fact that in recent 7.5 builds the http properties are ignored unless they are set by editing jetty.xml.
I wonder if the supplied jetty.xml  could use <SystemProperty>. Something like:
 
  <New class="org.eclipse.jetty.server.nio.SelectChannelConnector">
   <!-- host sometimes needed in PaaS envronment -->
    <Set name="host"><SystemProperty name="org.basex.serverhost" default=""/></Set>
        <Set name="port"><SystemProperty name="org.basex.serverport" default="8984"/></Set>
        <Set name="confidentialPort"><SystemProperty name="org.basex.??" default="??"/></Set>
        <Set name="maxIdleTime">60000</Set>
        <Set name="reuseAddress">false</Set>
        <Set name="Acceptors">2</Set>
      </New>
/Andy


[1] http://docs.basex.org/wiki/Options