Dirk,
Thanks for your reply. Here's a simple example. When I run this query with Saxon HE 9.6, the output contains a CDATA section, but when I run it in the BaseX GUI, there is no CDATA and the angle brackets are escaped. Has this serialization parameter been implemented in BaseX? 
xquery version "3.0";
declare copy-namespaces no-preserve, no-inherit;
declare default element namespace "
http://www.w3.org/1999/xhtml";
declare namespace output = "
http://www.w3.org/2010/xslt-xquery-serialization";
declare option output:method "xhtml";
declare option output:indent "yes";
declare option output:encoding "utf-8";
declare option output:cdata-section-elements "script";
let $turtle :=
<turtle>
    <![CDATA[
    @prefix ex: <
http://example.org/> .
    @prefix test: <
http://test.org/> .   
    ex:test1 a test:Test .
    ]]>
</turtle>
let $html :=
<html>
    <head>
        <meta
            content="text/html; charset=UTF-8"
            http-equiv="Content-Type"/>
        <title>Turtle Test</title>
    </head>
    <body>
        <h1>Turtle Test</h1>
        <script
            type="text/turtle">{
            $turtle/text()   
        }</script>
    </body>
</html>
return
    $html
> .