I've actually wondered a lot about this. I've always had the idea that Ohtori doesn't really function on a linear timeline. Nor is the existence of the campus solid. People impress themselves upon the landscape. Mikage is a perfect example of this - someone who became completely sucked into the unreality. So is Anthy, who exists in perpetual stasis. Akio even commented that she too was a phantom. What is Ohtori? I often wonder that. Is it an extension of the siblings? Is it a place operative on its own? Does it even take on its own character?

100 boys died there, essentially trapping them within the confines of that world. They were used as the tools of Mikage. Did their influence simply disappear at the end of the Black Rose saga? What happens to those who died in the false world? What about the previous disposed duel victors? It'd be rather interesting to think that they were all in sort of rift. As if they were stuck in a The Shining situation, in which everybody exists in their own correlating timeline.

I think the significance of the dead bodies represents the sacrifices of the dead boys. Mikage notes that they were necessary murders in his episodes. In order for the duelist to be transformed, each has to have a sort of symbolic Rose Bride that comes in the form of the recycled souls. And by Rose Bride, I mean someone to be their sacrifice for them to build their new ambition upon. SKU focuses heavily on sacrifice as a theme, and furthermore its futility.

The corpses also represent the Black Rose duelists' former selves, I believe. They travel down to their deaths and are reborn in Mikage's fashion. Luckily for them, their suffering is transitory.

The coffin being burned represents the futility of the sacrifice. Since the Black Rose signets bears the power of their dead former bearers, Mikage is disposing of both the "Rose Bride" soul and dismissing one of his experiments.