Good morning (CST),
I very rarely eyeball other folks' work but decided to took a quick gander to see what bugs you might have found since I hadn't seen you reporting any in this thread.
FYI: I cannot replicate the following reported bug (it works fine on my end even on bench testing PC's with fresh installs):
View attachment 3611739
You might want to verify on your end as Bonus I, S2 can be played (once unlocked) via both the VN's Gallery and via the Achievements screens. I checked the Cutscene as well in case that is what you are referencing, again with zero issue.
Otherwise I personally agree with the other 3 S2 bugs you mention.
Regards.