I believe, and i may be wrong, that this statement of apology comes in response of "new" information that emerge from the new report, which FIA has made known to Mclaren their concerns.
I disagree that there is nothing to apologize for. FIA has got much criticism (though understandable) for their investigation of Mclaren, with many accusing it purely as a "witch-hunt". However, that the investigations continually reveal more truths and information showed that while FIA is harsh, their actions were not unneccessary. Without FIA's unpopular insistence to monitor and interfer, we would not have known about the emails, and now, that more within the team in Mclaren knew.
If Mclaren has taken this stance from early on, much of this embarrassment could have been avoided. Rather than let FIA dig out things little by little... It's not nice a situation, regardless of whose fans we are.
It's unfortunate that this case seem to drag on forever. I had hoped for closure after the punishment being issued, but every few weeks, we have new developments that reveal more about the unfortunate case.
I'm sure many can forgive, even if they can't forget. All teams do wrong, at some point in history.
Dragging it on will not do us, FIA and Mclaren any good.
Next thing we know, maybe the Mclaren statement is a prank from some FIA-sponsored hacker?