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I would say so. Otherwise, we'd need Word of God, something not present in the work.
Most people involved in Game Studies who have studied BioShock do comment on it as a deconstruction of Atlas Shrugged and a prime example of Environmental Storytelling, yes. I would say the creator's intent is irrelevant.
"If you aren't him, then you apparently got your brain from the same discount retailer, so..." - FighteerTrope deconstruction is one thing— but one work deconstructing another work doesn't sound to me like a deconstructed trope to me. Sounds like something that does require Creator intent, and if there's no evidence of intent, it's an audience reaction to the work reminding them of themes from another work...
(But I may be getting blurred between this site's take on deconstruction versus literary theory/criticism)
Edited by ImmiThrax Covered in Star Wars Cleanup, Deadpool, and Web Video sand. I'm not coarse and rough, but I get everywhere.

I was wondering if Deconstruction, or other playing with tropes, have to be intentional. What if it's done by a writer who doesn't understand nor is trying to do it, but are trying to take a spin at it that winds up falling under such?