That's a fascinating analysis.
I haven't played The Last Guardian, so I can't offer any insight myself but this level of depth and interaction between gameplay mechanics and the plot should not be as unusual as it is.
Of course I might also assert that Trico's "disobedience" is the result of poor programming but like I said, I haven't played it yet.
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Imo his disobedience is simply the AI programmers trying to create a truly lifelike animal AI.