MessageDigestResourceVersion generates a hash of the file content which will be used as the version. As of now this doesn't take transformations by CSS/JS compressors into account.
This is problematic if you have a faulty compressor and your clients have already downloaded such a resource. By fixing the compressor you achieve nothing because the client happily keeps its faulty compressed version (by default for one year) as the hash didn't change. You either have to change the resource file (which is difficult for built in resources) or change the mapper path. The same holds true for other compressor improvements.
This issue isn't really limited to only compressors. If a resource output isn't only based on the resource file input then a wrong hash will be generated. IResourceVersion should always make the decision on the final output.