personally I don't think they will be retroactive. besides. there is one trophy in particular that suggests they will not be retroactive:
Complete the story mode within 30 hours or something. I reckon you will need a new game save.
I couldn't care less though. I don't have the game yet, so if they ARE retroactive, then that's great news for the people who have completed it already. if they are not, then I will simply start from the start as planned.