As part of some experiments, I compared two JSON files:

$ java -jar tools-java-1.1.0-jar-with-dependencies.jar CompareDocs compareOutput.xlsx ../testResources/SPDXJSONExample-v2.2.spdx.json ../testResources/SPDXJSONExample-v2.3.spdx.json

In order to understand the output better, I tried to remove a package from either of the files and check what changed in the output. I removed this section from either of the two json files:

{
    "SPDXID" : "SPDXRef-fromDoap-1",
    "copyrightText" : "NOASSERTION",
    "downloadLocation" : "NOASSERTION",
    "filesAnalyzed" : false,
    "homepage" : "http://commons.apache.org/proper/commons-lang/",
    "licenseConcluded" : "NOASSERTION",
    "licenseDeclared" : "NOASSERTION",
    "name" : "Apache Commons Lang"
  }, 

The observed result was:

• The output was unchanged if the package was removed from only one of the two input files. The package SPDXRef-fromDoap-1 was still shown in both columns
• When removed from both input files, the package vanished from both columns (as expected)

I would have expected no output in the v2.2 column concerning package SPDXRef-fromDoap-1 after removing it from the v2.2 file.