I can't help you much with most of your concerns, but I can tell you, that Aegean has, as of about 18 months ago, started "merging" (or "marrying" if you will) the outbound and inbound legs of a combined (return / open jaw) booking in such a way, that one can't be changed without the other one getting changed too (even if you only want to change one of the, the other simply gets rebooked/reissued for the same date + same flight, but using the change T&C's according to the ticket type and of course by paying any fare difference or re-booking fees. They did so silently and even though, as you pointed out, no discount is offered when booking return tickets (I believe there was at some point and only on a few selected routes a 10% discount on return tickets over 2 one-ways, but I don't think this ever beczme a "thing", at least not for my routes).

What's interesting here is that the "unflexible" part of your trip is already in the past! Had this been 2x Flex, then you would have now been able to change the 2nd flight without any "fare difference" charged for the already completed flight. But since this was the ticket mixture that it was, I just have no idea what to expect ​​​​​​.