How do I interpret the results of the config changes for the Sitecore Express Migration Tool?

Question

I have run the Sitecore Express Migration Tool 3.1 to migrate a 7.2 instance to 9.0 and I am very confused by the different diff and disabled migrated config files. I have read the EMT guide (specifically section 4.1.1) but I still don't understand what I am supposed to do with these migrated config files. Here are different examples...

From the web.diff.config.disabled file:

  <log4net>
<appender name="LogFileAppender">
  <!--EXPRESS MIGRATION: The node has been deleted-->
  <!--<encoding value="utf-8" />-->
</appender>
<appender name="WebDAVLogFileAppender">
  <!--EXPRESS MIGRATION: The node has been deleted-->
  <!--<encoding value="utf-8" />-->
</appender>
<appender name="SearchLogFileAppender">
  <!--EXPRESS MIGRATION: The node has been deleted-->
  <!--<encoding value="utf-8" />-->
</appender>
<appender name="CrawlingLogFileAppender">
  <!--EXPRESS MIGRATION: The node has been deleted-->
  <!--<encoding value="utf-8" />-->
</appender>
<!--EXPRESS MIGRATION: The node has been deleted-->
<!--<appender name="PublishingLogFileAppender" type="log4net.Appender.SitecoreLogFileAppender, Sitecore.Logging"><file value="$(dataFolder)/logs/Publishing.log.{date}.txt" /><appendToFile value="true" /><layout type="log4net.Layout.PatternLayout"><conversionPattern value="%4t %d{ABSOLUTE} %-5p %m%n" /></layout><encoding value="utf-8" /></appender>-->
<!--EXPRESS MIGRATION: The node has been deleted-->
<!--<logger name="Sitecore.Diagnostics.Publishing" additivity="false"><level value="INFO" /><appender-ref ref="PublishingLogFileAppender" /></logger>-->
<logger name="Sitecore.Diagnostics.Search">
  <!--EXPRESS MIGRATION: The node has been added-->
  <encoding value="utf-8" />
</logger>
<logger name="Sitecore.Diagnostics.Crawling">
  <!--EXPRESS MIGRATION: The node has been added-->
  <encoding value="utf-8" />
</logger>

What is this telling me? I see a number of The node has been deleted comments. And I see a few The node has been added comments. I don't understand what action I am supposed to take here on my new migrated 9.0 instance. Am I supposed to go and add or remove things from my 9.0 instance? I guess I don't understand what The node has been deleted and The node has been added mean.

Here are some more examples:

    <!--EXPRESS MIGRATION: The node has been added-->
    <httpRedirect enabled="false" destination="" httpResponseStatus="Permanent" />
    <!--EXPRESS MIGRATION: The node has been added-->
    <httpProtocol>
      <customHeaders>
        <add name="X-Frame-Options" value="SAMEORIGIN" />
      </customHeaders>
    </httpProtocol>
    <!--EXPRESS MIGRATION: The node has been added-->
    <rewrite>
      <rules>
        <rule name="LowerCaseRule1" enabled="false" stopProcessing="true">
          <match url="[A-Z]" ignoreCase="false" />
          <action type="Redirect" url="{ToLower:{URL}}" />
        </rule>
      </rules>
    </rewrite>

The other part are all of the disabled config files in the include folder. I imagine that I need to go through those one at a time and decide if I want to still include those in the 9.0 instance.