Yes, the airports in Greece use their own local system and so OLCI doesn't work outside ATH and SKG. The other airports all require you to turn up at the check-in desk even if HBO. Apps don't work either. Pre-paid seats will be honoured, as will seats selected in MMB due to status or ticket conditions.

At this time of the year I wouldn't count on an empty seat, but you are in an E190 so the leg room is about as generous as it gets for shorthaul. BA aren't selling seats on that service. Well Y1, which means almost zero. If there is an empty seat to be found it may be right at the back (row 23 and 24), which bearing in mind they disembark front and rear at LCY isn't necessarily bad.