Issue Comparing PDF's with Aspose

I am having an issue when comparing 2 PDF’s with Aspose.Words. When calling the .Compare() method, our code will create a “diff” PDF if the PDF’s are not equal. I am seeing an issue where the 2 PDF’s compared look identical to the human eye, but the .Compare() method will fail with 80 + revisions, and create an output (diff) PDF. The issue is that this output diff PDF created by Aspose does not show any differences (no red strike outs), and is rendered much differently than either of the 2 compared PDF’s. Can someone help with this issue? We have a Aspose.Total license.I cannot upload the PDF’s to this post as they have PHI.

Here is the code for reference:

SetAsposeLicense();

Document baselineDoc = new Document(baselinePdfPath);
Document generatedDoc = new Document(generatedPdfPath);

// There should be no revisions before comparison
baselineDoc.AcceptAllRevisions();
generatedDoc.AcceptAllRevisions();

baselineDoc.Compare(generatedDoc, "Reports PDF Comparison", DateTime.Now);

if (baselineDoc.Revisions.Count.Equals(0))
{
    logger.Debug("Both PDF's matches");
    return true;
}
else
{
    string filePath = Path.Combine(outputFilePath, string.Concat(outputFileName, ".pdf"));
    baselineDoc.Save(filePath);
    logger.Debug($"There is a mismatch between the PDF's, the differences is saved in the file - {filePath}");
    return false;
}

@aagibbons89 Aspose.Words is designed to work with MS Word documents. MS Word documents are flow documents and they have structure very similar to Aspose.Words Document Object Model. But on the other hand PDF documents are fixed page format documents. While loading PDF document, Aspose.Words converts Fixed Page Document structure into the Flow Document Object Model. Unfortunately, such conversion does not guaranty 100% fidelity.
I am afraid there is no way to 100% preserve PDF document Layout after PDF->Aspose.Words DOM->PDF roundtrip.
Regarding PDF document comparison using Aspose.Words, though PDF document might look the same visually, their structure might be different, that leads into the different DOM build by Aspose.Words and as a result the differences in document comparison.