The fundamental disagreement was in relation to the pre FFP wages and how they were allowed to be offset, we used the original toolkit but UEFA decided it wasn't clear enough and republished it but crucially, after we'd submitted our figures. using the original toolkit we would have scraped through, the new version caused us to just fail so that we couldn't offset them which had the effect of making us fail it massively.
This is broadly true but there's a minor, nitpicky point. We were always going to fail FFP because we were miles outside the acceptable deviation for the initial monitoring period, but UEFA had provided that teams would avoid punishment if they could demonstrate that they'd have been within the acceptable deviation after wages paid under player contracts predating 2010 were deducted. For what were presumably PR reasons, we tried desperately to make that cut but, as you say, were sawn off at the knees by the retrospective amendment to the rules.
I'd say it's probably a good job UEFA did change the rules, ironically. The settlement agreement allowed us to start again in 2014, with a target relating only to the next two years - as opposed to having to factor in losses from previous years in the context of a three year assessment period. But most important is the fact that now, with them coming after us in the wake of the Der Spiegel coverage, without the settlement agreement, everything from 2014 would have been up for grabs in terms of making a case against us. It would definitely have made their life much easier in the current situation.