it sounds like the other episodes (the ones missing from disk) are probably unmonitored
it can also happen when only 2 eps have been aired and there are 78 more to be aired, its still 2/2, not 2/80 (ie, only aired eps are counted)
the missing from disk flag is most likely because you did download them at one stage (or manually put them there), then deleted them from the disk - you also have sonarr setup to automatically unmonitor deleted eps (so it doesnt try to download them again), and once unmonitored it no longer counts towards the total
i’ve always thought the x/y display was weird due to missing episodes not being counted once its unmonitored (be that season or individual eps) as a season has a fixed number of eps that should be downloaded, it shouldnt matter if you monitor/unmonitor them, the amount should always be the same.
the unaired eps not counting makes a sort of sense but it screws up the season pass page display as you have no idea if there are other eps still to be aired for the latest season, or if it has ended