Updating global extensions via EM silently leaves potentially risky code on the server.
Since EM in 6.2 does not provide any information about installation place of Extension (typo3/sysext, typo3/ext, typo3conf/ext) you won't notice that there is old code left on the server.
If you update an extension which is globally installed, EM silently installs to local directory, leaving the global directory untouched.
In case of security fixes in such extensions, the security-leak just remains silently on the server, no chance to find that out via TYPO3.
IMHO we should AT LEAST have information about this bad and potentially risky behaviour in the extension manager.