I am looking for a rule-wise explanation of the logic as to why your deflection bonus (e.g. a shield) is counted in your flat-footed AC.
From what I understand, being flat-footed means you didn't see the attack coming, and are unable to react to it, so only your passive armor counts (meaning the opponent still has to hit 'hard enough' to actually pierce your protections). In that context, how would you be able to parry? You can't dodge, you should not be able to parry as well. I realize a shield can be useful if you can't dodge because you 'just have to raise it'; The problem is not every flat-footed situation should allow for a shield to be used.
Pushing things to the extreme: consider an invisible character sneaking to a guard. The combat is not started, the guard is unaware of any danger. The character is behind the guard, unseen, unheard, and ready to hit. Why would that guard's shield be taken into accout? Why would his armor even be? The character should be able to stick its dagger in the guard's neck (or any other not-armor-covered part) and deal a good amout of damage without having much armor to go through.
If I'm not mistaken, according to the rules that guard should be flat-footed. This means if the character attacks the guard, the rules consider he is able to: sense the attack, turn around, deflect the attack with his shield.
From the logic of that context, I'd say that guard should be considered defenseless, shouldn't he?
My table had trouble with a player recently contesting the logic of that rule (and honestly I can't blame him), and we had trouble making him accept that yes, his paladin's shield was useful against that ogre's enormous club.