Another detail is that, when the domestic leg is booked together with an international one, it will automatically get Aegean flight numbers.
If we are talking complot theories - one difference is that with OA flight numbers one cannot access any lounge in ATH besides the Aegean one. That will save OA/A3 about 20 euro as their own lounge will most probably have much lower costs. And as such it is understandable - many domestic flights can be booked from about 25 euro all in!