Indeed, the game is mysterious in some aspects.
I don't think that VKing people has significant impact on the story.
If it does, then it can lean McCoy's personality to either REPLICANT SYMPATHIZER or TRUE BLADE RUNNER.
But, if you play true Blade Runner, you may decide to retire a subject once VK tells you he/she is a rep. And killing people DOES alter the story.
Some people are easier to test than others. Grigorian can be difficult subject to test , but he's always human. If you test Lucy in the sewers, you will always get some result, no matter what questions you ask and no matter whether she's human or replicant. Bullet Bob is the most difficult subject. There is really no clear evidence whether he's rep or human - it all depends on how do you callibrate the machine and what questions you ask him.
On callibration - again, results for some people are sensitive to manual/automatic calibration and for others they are not. Results of Bullet Bob are very sensitive to even automatic callibration - second callibrating question will set the response marker to a higher point, possibly altering the result. How the manual callibration alter the results is rather obscure, but I think that the more to the right you set the marker, the stronger response threshold machine takes into consideration. Stronger response = more human. I think.
Modified KIA.... I always thought that if you upload some "undesired" info (like DNA information or Photo of McCoy near moonbus) into the mainframe, Steele will get it and behave accordingly. But it doesnt' seem to matter much whether ypu upload them or not. Perhaps the developers didn't implement it's story-altering possibilities as they expected...
Still it's nice to have a modified KIA just for the sake of it.
