Isn't the article about security, not fidelity. Who is going to bother trying to hack FLAC files? Hackers go after the big users like Microsoft programs and maybe Itunes.
Multiple Vulnerabilities In FLAC
They found 14 vulnerabilities in the processing of FLAC.
See http://research.eeye.com/html/advisories/published/AD20071115.html
See http://research.eeye.com/html/advisories/published/AD20071115.html