There is a Preference (File\Preferences\Source control) that is set by default to binary encode all the non-file based content. It is set this way to ensure that by default, we should not lose content on DXL round trip. However, if you know your application and know that text based DXL is sufficient, you can uncheck that box and get text based DXL - which will certainly have a more meaningful compare!
Hope that helps!