Will you have checked luggage? If you do, will Aegean interline on separate tickets?
With separate tickets, you have 2:40 less the time that check-in and bag drop closes: say 45minutes?
For 2:40 between flights I would spend the €62
Presumably you have looked at other airlines
http://www.gcmap.com/mapui?P=MAD-ATH-JTR+&MS=wls&DU=mi
https://en.wikipedia.org/wiki/Santor...tional_Airport