I then in writing this post looked up Tchort for the wiki and found that it apparently means Devil in slavonic languages
Can't say for other languages, but in russian it's more like a minor demon than devil.
Also, Six is about as far from angel or saint as you can get. Though he does pull that sanctimonious "i know better than you" attitude very well, so who knows.
I found the end-game of my first two playthroughs good up until Core city.
Um, maybe i didn't understand you, but core city is not an endgame. It's available right after the prologue (if you can call it that way). Also, it's bigger and with more stuff to do than institute, so here is that.
P.S. You are reading too much into this. Did you have strict religious upbringing?))