Do you not check in online? If the bags are tagged all the way through, why do you need to go to the counter? You can just take your boarding pass and go straight to the non-schengen area.

Also, I don't think I have ever seen gates close 20 minutes before departure on Aegean. They usually don't start boarding until about 30 minutes before, and boarding usually takes more than 10 minutes. So if your flight lands on time, you definitely should be okay.
However, that being said, I would highly recommend taking an earlier flight if possible, if only to be able to enjoy the new non-Schengen lounge for a bit. It is a nice space and since you are flying in business, you should try it.