As you probably know, stays “under a residence permit or a long-stay visa” (including a work holiday visa) do not count toward the 90-day period but it's not entirely clear (to me, at least) if that also includes stays outside of the country that issued the long-stay visa.
But it doesn't matter in this case as there are more than 90 days between your trip outside Germany and your visa-free stay in the Schengen area! You could in principle travel to Greece in June and then stay 90 days in Germany three months later without ever breaking the 90-days-in-any-180-day-period rule even without the long-stay visa. You can verify that with the online calculator.
Additionally, there will be no obvious trace of your trip to Greece (no passport check, no stamp) so even if you stayed too long/later in the year, you might still get away with it.