This is a take I never really thought about.
I always felt like it was not ruin directly exerting the force of the shard, but was a ritualistic way of tapping into the essence of the ruin shard. The magical nature of the spike meeting with a ritual that symbolizes the aspect of ruin, that something can only be created out of the destruction of something else. I think that the nature of the shard's relationship with Scadrial would always be inherently there, whether harmony wanted to stop it or not. But this is all theory based on my interpretation of the book, I can't cite any interviews or sources for this.
I would suspect that the "twisting" of the being isn't entirely physical. If I recall corrrectly when Marsh was made into an inquisitor, since each spike has to be driven through the body of an allomancer possessing the power to be imbued, and that the traumatic nature of the ritual would twist the soul of the inquisitor, much like ritual abuse does in real life. And as for the organs rearranging, I would think that the power of Ruin would, when it was invoked through the ritual, protect the organs that would be needed and push them out of the way as the spike is being driven in, no explanation why, just a structural detail like Swimmingly said.
...but maybe someone who has the adventure game has more information about it?