Actually I think the "reasons" are that the current Boeing CP likes to put stuff like this in his newsletter and the previous (and current) Airbus CP hardly puts anything in there apart from A350 stuff. Likely it had been happening for years and even if ATC were telling the company the "we are Cathay, we know best" attitude of old probably meant that it never went beyond the chief pilot's e-mail trash bin.
Even now if it wasn't for the newsletters no-one would know anything. ATC don't question those flights over the radio so even the crew themselves don't know they've done it.