I did both the upstream and downstream ending first without seeing the final chimera scene. I don't remember seeing Yaldukra in upstream, but I distinctly remember the whole "I'm guessing that you had something to do with this," conversation in downstream. I also remember being really confused when he spoke about how his tattoo reacted to... something that sounded likely sexual in the Side B content.
Then, I went back and finished the chimera scenes before going downstream again, and I didn't initiate any conversations with Yaldukra because I'd already seen them.
The extra chimera scene was the only one that I hadn't been through by the first go-round, though, so maybe it had something to do with that? I also remember running into some chimera in that well-lit area right nearest to the extra scene, but I never caught up with them, nor could I get them to reappear. My guess would be either THAT... or that I at some point played the game in a fugue state and had unlocked all of the chimera scenes all along. (Although the latter wouldn't explain how I went back and saw the scene after I re-loaded my save; I only saved once before the point of no return.)
Sorry if I'm not much help with identifying the issue. I haven't noticed that anyone else has claimed the same, fortunately, so maybe it's just some sort of fluke with how I handled the files.