To summarise, addressing your requirements:
- Comparison tool that can compare XSD files: Yes
- Can identify changes in structure, not just content of XSD files: Yes
- Can ignore expected changes: Yes
- Orderless comparisons; avoiding false positives from moved elements: Yes
- Compare all files at once: Yes, through batch processing
- Produce a report with the details: Unclear what is needed here
XML Compare, developed by DeltaXML, is a structurally aware XML comparison tool that is able to identify change in both the structure and the content of XML files, including XSD.
In instances where elements have moved in the file but the order of said elements is not significant to the comparison, XML Compare has built in functionality for Comparing Orderless Elements. This can be customised extensively using XSLT as needed.
When you are expecting changes that do not need to be identified as change, you can use XML Compare's built in Ignoring Changes functionality which can again be customised using XSLT.
For bulk processing of your files, although XML Compare only compares files 1-to-1, it can be run via the command line, REST API and Java API. This means that by writing a batch file to queue up comparison operations, or if you use the REST API the comparison operations will be queued automatically.
Finally, to address your need for a report summarising the results, this depends on what you mean. XML Compare is capable of producing HTML reports from diff outputs that highlight changes in-line or side-by-side. It sounds however like you may be looking for a more statistical report on the results of the comparisons, for which XML Compare does not currently have a facility. It is worth noting however that the diff outputs produced by XML Compare are valid XML, and can be readily processed to identify the change attributes in the file.
Disclosure: I am an employee of DeltaXML.