I think what you've pointed out illustrates why the 'release a game a little bit at a time through Patreon' model just doesn't work with truly branching stories.
Skyrim maybe isn't the best example for my explanation, but let's go with it. With a 'released when it was finished' game like Skyrim, the developers could take the time to put everything in the game and have it all ready for the player when they began playing. No matter what choice you make or path you take in the game, that content is finished and waiting for you.
With a game that's put out in pieces like BaDik (or 99% of other games on this site), the creators are faced with two choices if they want truly diverging paths based on actual choices... either they have absolutely massive updates that take a very long time to release (that get bigger and bigger and bigger as more of that divergent content appears in the game) or they release content patches that do not have content for all choices and paths (thus locking a chunk of players out of that content). Basically, imagine if the Derek-Sage-Bella choices in Chapter 4 were released as separate content updates in that order... if you had chosen Bella, you couldn't play the first two updates and you'd just have to wait while others played the new content. Either way, you end up with a bunch of very, very unhappy Patrons and players.
So, the only real option is, as others have mentioned, the illusion of choice... either by having all roads lead to the same 'big' moments and eventual ending (as BaDIK will almost certainly continue to do), or as was the case with AL, simply swapping which characters appear in the same scene based on which choices were made (meaning the hospital, locked room, and funeral scenes all happened basically the same way but who was with you in those scenes changed).
Again, I don't think this is the fault of DPC (especially since, as others have mentioned, he's just one guy doing all this stuff himself)... it's just the cold facts of the release model of Patreon games.