Just played through this, and wow! I did not see that ending coming at all, but I did follow the breadcrumbs they were leaving regarding Dysis potentially being Clover's sister, so I thought it would stop there.
One thing I think you may have missed is although we are meant to believe near the end that Dysis was an actress (as was the original plan as explained by Andre to Vincent, also strengthened by Dysis stating she would do anything for money), before the credits, Andre reveals that he did not actually tell Dysis about the plan because he wanted her relationship with Clover to be authentic or something along those lines. I think this makes sense with what we see in the game because there are two key Dysis/Andre scenes where there wouldn't be much reason for Dysis to be acting since Clover was not present. He then says that Vincent will be mad about that but that it's his punishment for his past behavior.
I had to run back through to get the two missable trophies and it was interesting seeing the details like the fake monuments as well as the broken ones in the background, knowing the full story.
Not a perfect game (some of the dialogue and exposition was a bit clunky) but absolutely gorgeous and I really enjoyed the experienced, though it was a bit depressing in the end. Would definitely play another game by this developer