Currently NodeFilter is not applied to DocumentType so you cannot suppress the comparisons. There may be even more Nodes missing, a cursory look through DOMDifferenceEngine says it probably is the only one but a second pair of eyes won't hurt. I don't think there is any good reason to apply it to Document itself as this would simply skip all comparisons altogether.

See also xmlunit/xmlunit.net#26 which may provide a solution that "just" need to get ported.