When comparing signatures of two PDF documents using the PDFUnit release 2015.10, only the names of the signatures are compared:

<testcase name="haveSameSignatureNames">
  <assertThat testDocument="test/test.pdf"
              masterDocument="master/master.pdf"
  >
    <haveSameSignatureNames />
  </assertThat>
</testcase>

Further comparisons will be possible in future releases.

Use the ExtractSignaturesInfo to extract details of signatures and certificates. See chapter 9.10: “Extract Signature Information to XML” for more information.