Can I use a Diff viewer to compare two XoomXML files?

You can, but you need to prepare the files first using either Xoom Explorer or Xoom Processor. Use a Diff viewer when you want to see the detail, rather than an overview, of what exactly is different.

Why do I need to prepare the files first? A Diff viewer simply treats the XoomXML files as text and will consequently show every difference, even those that are irrelevant for the purposes of configuration management. Examples of irrelevant information would include IDs for Collections, and keys. The way round this is to transform both files first to remove irrelevant information.

Do this by applying the RemoveEnvironmentSpecificInformation.xsl report to both XoomXML files, using either Xoom Explorer or Xoom Processor. The transformed files can then be loaded into a Diff viewer and meaningfully compared.
Note: The RemoveEnvironmentSpecificInformation.xsl report does not produce valid XoomXML. A file transformed with this report should never be deployed. Its sole purpose is to ease comparison.