I tried the booking on Aegean's website as a "more options" (usually used for open jaws) and couldn't get the system to book the two flights on the same day.
It would be a bit of a calculated risk, also depending on the time of year, to book these separately and just hope that either there won't be any delay, or that Aegean will grant you similar rights as if you had booked both flights together.

Or is it a case of the same aircraft flying both these segments consecutively? I think, in such a case, even booking the flights separately would include very little risk.

By the way you can see the booking class on Aegean's website, so perhaps that's another indicator of what the OTAs are also selling. It seems that only Flex and comfort flex tickets are being sold. I also tried the ITA matrix and I believe they showed the fares as "Flex" (but I'm not an ITA matrix expert by any means).