I think you're wrong. It's a bit vague with all the unfamiliar systems (I have no experience with OS X), but root is mentioned in a few places:
> "The allow-root property specifies whether a right should be allowed automatically if the requesting process is running with uid == 0. This defaults to false"
So the agent does not (by default) make an exception for applications running with uid 0. It does not say anything about modifying a certain file, it's just about the agent (if I understand it correctly).
> "In other words, if allow-root isn’t explicitly set, the default is that even a process with root user privileges does not have the right to perform that operation. Since that’s not specified in the default shown above, then even root couldn’t add Dropbox to the list of apps in Accessibility preferences."
Same thing again. Agent won't allow, but file permissions are not mentioned.
> "Root wasn’t allowed to override Accessibility, and authenticate was on, so it couldn’t be this way that Dropbox was hacking my mac."
Same again.
And that's all places where root is mentioned. Later on, however, sudo is used:
> "To insert an app in the list, you grab it’s bundle identifier (in the case of Dropbox, that’s com.getdropbox.dropbox), and issue:
> sudo sqlite3 /Library/Application\ Support/com.apple.TCC/TCC.db “REPLACE INTO access VALUES(‘kTCCServiceAccessibility’,’com.getdropbox.dropbox’,0,1,1,NULL, NULL);”"
So sudo, which makes a command run as root, can modify that database.
And as far as I know this makes sense, because at least in Linux file permissions are simply not checked when uid is 0 (root user). Darwin/BSD might differ, but my unix family tree knowledge doesn't go that far.
Also, how else could Dropbox do it? As mentioned in the article, one of the helper applications contains an SQL statement (see the part about running "strings"), so it does seem to be directly modifying that database.