Hi, so I did a few tests and here are the results:
1. So this bug happened during my very first playthrough (so white text, and no Skip prologue/play prologue first choice). I tried with a new save with the same choices (but this time since it's not my first playthrough, text was gray and first choice is Skip prologue/play prologue) and indeed, this time the choice appears! But I still have a save (my very first playthrough) where this choice is missing. My theory is that this choice does not like being in the 5th position. If it's 6th due to the Skip prologue/play prologue choice, it's happy and showing, otherwise no xD.
2. This one is very mysterious to me now. I also cannot recreate it, even though I used the same save it happened with??? It used to happen anywhere in the story, regardless of the chapters: as long as I rolled back just before clicking on Flowcharts, I had the error. But now it stopped happening for some reason. But if you say that's a typical Renpy error, then I guess you cannot do anything on your end anyways. It's not very important, I could go back to where I stopped by clicking Rollback on the error, so nothing was lost. It's very strange though.