For the future I'm pretty sure that the F5 debug button should have fixed that but in any case yes those are similar problems in the game's architecture.
Z - Reborn I think this is solved in 3.99.
Didn't know about F5; useful to know. Would also be useful to have a description somewhere in-game of what the stats do. Some are obvious (time/energy/blood) but others less so. For example, I still have no idea what the double chevron on the top of the second column means.
Other quick question. In my 3.987 run, I found a blonde girl in Watson Hall on campus grounds; the building became available once Tea was acquired. She seems to have some relation to Mara but other than some talk options, nothing is available. I didn't have Mara with me when I found her since I only travel with her when I need her to lockpick a quest location.
So it this a bonus girl that was not properly locked down for the public release ? A future character that is not used yet (i.e. for after Mara is fully converted) ? Or some interaction that I missed because I didn't have Mara with me ?
Also, I could not do get Tea to travel with me at the start of Chap. 4: she was my initial guess as a helper to find the quest book, which made sense to me since she's an assistant librarian. Once I interacted with Brendan to actually get the book, she became available. I know Tea is optional but she seems to be a reasonable alternate method of getting library access so I think that should be added and/or fixed.