You're right. That is the way the current episodes are coded.When you choose to kill JD it seems to assume you've chosen all the red choices before that point, vice versa on the blue choices for sending JD to prison, which has Tracy keep mentioning her forgetting to get a morning after pill before that choice as well, even if you fucked her ass the first time instead, which is very bad, as a story focused game like a VN needs a consistent story that takes into account which choices you made and which you didn't make.
I think the inconsistencies in the beginning can easily be fixed with the choices having flags, and have dialogue be changed by having it look for whether the flag was activated or not, that's what all the big VNs I've played do, and it works perfectly.
If I go back and recode the early episodes, it will break everyone's saves. I'm going to do a remaster of the early episodes after the completion of Chapter 1.