Massive creds for having a actual philosophical-theme in your story, I'm not sure if that's EVER been done in a video-game before.
In really good movies the entire story is often written simply to demonstrate a "moral of the story", for example the team who got together to eventually write Lion King first decided on what part of childhood they wanted to give a life-lesson about BEFORE they even decided the story had anything to do with lions!
they first wrote the life-lesson (which IMO is "Hakuna matata, how sometimes when you have a painful experience while growing up the best you can do is to put it behind you and enjoy life like it never happened, yet when you've finally grown up then you must gather courage to deal with it.") and then they tried to come up with the best setting, characters and plot to convey that life-lesson,
when you hear hollywood-stories like that you truely realize why video-games stories comes out flat, that sort of depth is just not of interest to the project lead in most game-project. (shit I worked on a AAA-game where they hired a outsource writer to write a first draft AFTER we finished making all the levels!!)
I'm not entirely sure I understood what your exact message was with the game, as the dialogue towards the ending confused me a bit, but in any way it felt like the story was crafted around a philosophical-topic, that it wasn't just "ok let's begin, I need a cool character, ok now I need a cool inciting incident, ok now I need a good twist and a cool ending" but it was more like "what scenario of any universe could really put this philosophy of human behavior to the test?".
So I really liked the fact that it explored a subject, altho again I didn't quite understand what your exact meaning was, where you trying to say that it's not JUST life-experience (or in this case implanted memories) that shape your future as a good person will always try to make good-ish deeds out of it (which he did upon escaping the boyakata) in other words that ppl can't fully blame a f'ed up childhood on their evil deeds.
or am I completely projecting way too much thought into this? was the memory-theme there just so you could spin a cheap twist at the ending?