The calculation is based on amortisation of the players value. So the lumps and bumps of ins and out dont really impact as much as you would expect. And as above, lots of expenditure is excluded so hard to know the real position.
As to why we 'took a pinch' I assume that we had a decent argument but they make the rules, to get in a fight is not a good strategic move for either party (if we beat them in court it would not have been the end of the issue and you could argue the negative PR would be equally as bad as just accepting a big fine). I think the 'pinch' was basically a settlement where we accepted a sanction we could live with (small fine and squad restriction) on the basis we did not challenge through CAS or anything else. My guess is the same arguments are ongoing now around teh legal basis for anything they want to do and if we accept a sanction or fight it. My guess is that the leaked material can not be used in court and as we accepted a sanction already they have little ground to stand on - but that is a guess. None of us know what they have.