If it can break when it's freshly downloaded, with no updates and with only the files it came with
It doesn't break when freshly downloaded from Patreon. I did that and played v027 from start to finish without the problems you described! However on this forum the uploaders do things to the official downloads which can introduce problems. For example they upload the wrong savegames. This has happened in the past. That is not a bug in the official version, so it can't be fixed by the developer...
If you had downloaded the official version it didn't include savegames, so when you start that one you get a clean savegame without any issues. As said I did that and I'have all the bookmarks from the incest path. I can give you one so you can see for yourself that if you have problems it is introduced by not starting correctly. Some people install old bookmarks and then start a new game, which means that there "new" game is based on bugged bookmark which give the problems you describe. So I'm still not convinced that you did everything correctly...
Again I can upload a savegame at roughly the point you want to continue. It will contain the state of the game as I'm playing -- see my walkthrough -- but at least you can talk to Hoyt etc.
Edit:
Because you didn't upload your savegame I can't check if you did everything correctly. But because you immediately harped about a bug, I think you unknowingly used a non Patreon version of the game and didn't t check if you started correctly a new game...
So it is up to you to either upload a savegame for me to check or to accept my offer to give you a savegame which works and is roughly at the point were your are...