Unless I missed it, this article seems to not refute the most fundamental point: MD5 was never broken for encryption. Hashing is not encryption.
Moreover, MD5, SHA-1 and SHA-2 contain a block cipher function used in the Davies-Meyer mode of operation.
The internal block cipher function can be extracted and used in any other mode of operation possible for block cipher functions.
Because of these possibilities, many older laws that have existed in various places, prohibiting the inclusion of encryption in software products, but allowing secure hashing functions, have been completely misguided.
The point is that MD5 is no good if there's any way an adversary might want to subvert it. It's fine if you just want to use it for hashing your own documents, but as soon as there's an incentive for someone to substitute one document for another, MD5 is problematic.
That's certainly the case for encryption, but it's also the case for these legal document records.