> The author also doesn’t suggest what should be used instead to encode structured data, or perhaps more importantly what should have been used to encode graph like things such as map/lists/objects in the 2000’s.

That’s easy: S-expressions. Steve Yegge wrote about this in 2005: https://sites.google.com/site/steveyegge2/the-emacs-problem

Would you rather have:

    <?xml version="1.0" encoding="utf-8" standalone="no"?>
    <!DOCTYPE log SYSTEM "logger.dtd">
    <log>
    <record>
      <date>2005-02-21T18:57:39</date>
      <millis>1109041059800</millis>
      <sequence>1</sequence>
      <logger></logger>
      <level>SEVERE</level>
      <class>java.util.logging.LogManager$RootLogger</class>
      <method>log</method>
      <thread>10</thread>
      <message>A very very bad thing has happened!</message>
      <exception>
        <message>java.lang.Exception</message>
        <frame>
          <class>logtest</class>
          <method>main</method>
          <line>30</line>
        </frame>
      </exception>
    </record>
    </log>

or:

    (log
     '(record
       (date "2005-02-21T18:57:39")
       (millis 1109041059800)
       (sequence 1)
       (logger nil)
       (level 'SEVERE)
       (class "java.util.logging.LogManager$RootLogger")
       (method 'log)
       (thread 10)
       (message "A very very bad thing has happened!")
       (exception
        (message "java.lang.Exception")
        (frame
         (class "logtest")
         (method 'main)
         (line 30)))))