For a while I tried to consider the logistics of recording my session and OBS with a third program to show it in action and how I could maybe get you logs of it happening, but then my brain exploded???
You mentioning GPU physics gave me an idea: I switched from the NVENC (GPU-based) OBS encoder to a CPU-based x264 encoder... but the same thing happened, so that theory's out the window. However, I did find out that non-fractal structures (at least the boat) are immune to this collision issue.
Really, like I said, it doesn't matter - display capture works just fine and I really, Really dig this game and can't wait to see how it develops and your future projects. If the problem fixed itself without restarting the game I'd have an unconventional little noclip cheat on my hands!!!