I wrote and released a Windows application that specifically solves the problem of comparing and merging XML files.

Project: Merge can perform two and three way comparisons and merges of any XML file (where two of the files are considered to be independent revisions of a common base file). You can instruct it to identify elements within the input files by attribute values, or the content of child elements, among other things.

It is fully controllable via the command line and can also generate text reports containing the differences between the files.

Focusing on the part that moved sections should be reported as no difference made me think of https://semanticmerge.com/, which doesn't compare XML-files, but C# and C code. And as it understand those languages it is able to display if code has moved and not changed.

This leads to an alternative approach for this question: Could it be possible to translate the XML into C# classes, and then do a semantic merge on the resulting code?

One possible approach, if this tool is not written already, could be to translate each and every element to classes, and each attribute (and body texts) to a string property within that class. If you want to ignore namespaces, then let your translator remove them in the translation process.

I translated the XML example given as proof of concept and got the following:

class soapenv__Body {
  class mes__GetItem {
    class mes__ItemShape {
      class typ__BaseShape {
          string body="IdOnly";
      }
      class typ__BodyType {
          string body="Textus";
      }
      class typ__AdditionalProperties {
        class typ__FieldURI  {
            string FieldURI="item:Subject";
        }
        class typ__FieldURI  {
            string FieldURI="item:Categories"; 
        }
      }
    }
    class mes__ItemIds {
      class typ__ItemId {
          string Id="AAMYAAA=";
      }
    }
  }
}

Then I switched the mes:ItemIds and mes:ItemShape and changed the text to Textus. Compared the following two files in Semantic Merge and got the following image:

In this image one can see the move, indicated by the M icon, and the change in text indicated by the C icon. Lines indicates where the different parts have moved/changed, and it possible to actually see the differences if they exist.

Note that Semantic Merge even though understanding C# code, isn't to strict on the identical class names of typ__FieldURI, which could be a nice features as XML can contain multiple nodes with the same name.

Summa summarum: Semantic Merge can correctly identify the XML as identical (or not) even though elements move, if you can convert the XML into a C# class structure.