All I can say that in the actual situation I alluded to earlier, I felt that my agency was honoured by the GM acceptance of setting aside the rules a bit so that the fictional situation could unfold in satisfactory and logical manner and had we not done so I would have felt that my agency was limited and violated.
But this is what I said before. You are petitioning an authority figure so you gain a special exemption. 'Please sir, do not apply any tariffs to my business at this time'. That isn't a high amount of agency, even if the authority figure says yes.
I generally feel that it is part of GM's job to make sure that the fiction unfolds in a manner that does not produce "this doesn't make any bloody sense" from the players, and if that requires overriding rules, then so be it. That is the coherence that allows players to make meaningful decisions, not the coherence of the rules. Granted, in a good game this should be in harmony most of the time, so that the expectations are one and the same, but this doesn't always happen.
I'm not sure what about your play example 'wouldn't make any bloody sense'. You said your character botched a resistance roll and took a lot of stress, meaning they suffered a trauma, meaning they would be out of the scene. That all seems perfectly logical to me. Are you saying there was something wrong with the framing, like the resistance roll shouldn't have been made? Or the consequences for failure should have been different? Was this not apparent or negotiable before the roll?