No worries. The thing with allowing the choice to keep popping up(like it would be in real life as you advises) is just regular vn mechanic to be only once with most of the characters, harsh, maybe, but is as to make decisions really matter to a character, I see your point, but is just the vn aspec of handling things.
As for the saving at any place, any time. This is because of the variables are handled, not possible at the moment without heavy investment into it, it is something that is wanted but that also requires a lot of focus.
Btw on the matter of the notebook, I referred to the calendar, not the quest log. There you'll be able to see important things like Toni's Bar date on Thursdays and Alice's visits on Wednesday.
Also, is ok to point out stuff that feel off, as long as the feedback is constructive and delivered in a well mannered way, there is no problem.
Have a nice one.